---
warning: DO NOT CHANGE THIS MANUALLY, THIS IS GENERATED BY https://github.com/duckdb/community-extensions repository, check README there
title: miint
excerpt: |
DuckDB Community Extensions
Bioinformatics extension for microbiome research - read/write FASTQ, SAM/BAM, BIOM, GFF, Newick trees, query NCBI, and more.
extension:
name: miint
description: Bioinformatics extension for microbiome research - read/write FASTQ, SAM/BAM, BIOM, GFF, Newick trees, query NCBI, and more.
version: '1.0.1'
language: C++
build: cmake
license: BSD-3-Clause
excluded_platforms: "windows_amd64;windows_amd64_mingw;windows_amd64_rtools;osx_amd64"
maintainers:
- wasade
requires_toolchains: "rust;omp"
test_config: '{"test_env_variables": {"MIINT_SIMD": "baseline"}}'
repo:
github: the-miint/duckdb-miint
ref: 5fbea2ab2bcd6888741d3752293293cc4202121e
variegata: 10f0fde06d091bc78939223dea928f4374d4fdea
docs:
hello_world: |
-- Extract 16S rRNA gene sequences from E. coli K-12 MG1655
-- Fetches genome and annotations directly from NCBI
WITH ecoli_16s_positions AS (
SELECT position, stop_position, strand,
attributes['gene'] AS gene,
attributes['product'] AS product
FROM read_ncbi_annotation('NC_000913.3')
WHERE type = 'rRNA'
AND attributes['product'] LIKE '%16S%'
ORDER BY position
)
SELECT concat_ws(':', read_id, position, stop_position, strand) AS read_id,
sequence1[position:stop_position] AS sequence
FROM read_ncbi_fasta('NC_000913.3'), ecoli_16s_positions;
extended_description: |
MIINT (MIcrobiome INTelligence) brings SQL to bioinformatics data analysis.
**Read bioinformatics formats as tables:**
- `read_alignments`: SAM/BAM alignment files
- `read_fastx`: FASTA/FASTQ sequence files (single/paired-end)
- `read_biom`: BIOM abundance matrices
- `read_gff`: GFF3 annotation files
- `read_newick`: Phylogenetic trees
- `read_jplace`: Phylogenetic placements
- `read_mzml`: mzML files
- `read_mzxml`: mzXML files
**Query NCBI directly:**
- `read_ncbi`: Fetch sequence metadata by accession
- `read_ncbi_fasta`: Fetch sequences from NCBI
- `read_ncbi_annotation`: Fetch feature annotations from NCBI
**Query and submit to ENA:**
- `read_ena`: Fetch accession level detail (BioProject, BioSample, etc)
- `read_ena_attributes`: Fetch full deposited attributes (BioProject, BioSample, etc)
- `read_ena_sequences`: Fetch sequence data (BioProject, BioSample, etc)
- Complete submission and submission lifecycle management support, see docs
**Alignment with SQL:**
- `align_minimap2`: Align sequences using minimap2
- `align_bowtie2`: Align sequences using bowtie2
- `align_mafft`: Align with MAFFT (parttree)
- `align_sortmerna`: Align with SortMeRNA
- `align_wfa2`: WFA2 pairwise alignment
**Sequence search, clustering, chimera checking, partitioning:**
- `search_sequences_vsearch`: Search a database of sequences with VSEARCH
- `cluster_sequences_vsearch`: De novo sequence clustering with VSEARCH
- `detect_chimera_uchime_denovo`: De novo chimera detection with VSEARCH
- `detect_chimera_uchime`: Reference based chimera detection with VSEARCH
- `rype_classify`: RY minimizer read partitioning
**Phylogeny estimation:**
- `phylogeny_fasttree`: Estimate a phylogeny with FastTree
- `tree_resolve_placement`: Fully resolve placements
**Mass spectrometry:**
- `massql`: A complete MassQL implementation
**Write to standard formats:**
- `COPY ... FORMAT FASTQ/FASTA`: Export sequences
- `COPY ... FORMAT SAM/BAM`: Export alignments
- `COPY ... FORMAT BIOM`: Export abundance tables
- `COPY ... FORMAT NEWICK`: Export phylogenetic trees
**Analysis functions:**
- SAM flag checking (`alignment_is_primary`, `alignment_is_unmapped`, etc.)
- Sequence identity calculation (`alignment_seq_identity`)
- Interval compression (`compress_intervals`)
- Woltka OGU classification (`woltka_ogu`, `woltka_ogu_per_sample`)
- Deblur amplicon denoising (`deblur`)
- UniFrac (PCoA, PERMANOVA) (`unifrac_pcoa`, `unifrac_permanova`)
- Faith Phylogenetic diversity (`unifrac_faith_pd`)
See the [documentation](https://github.com/the-miint/duckdb-miint) for complete details.
extension_star_count: 10
extension_star_count_pretty: 10
extension_download_count: 863
extension_download_count_pretty: 863
image: '/images/community_extensions/social_preview/preview_community_extension_miint.png'
layout: community_extension_doc
---
### Compatibility Matrix
This table covers all DuckDB releases that have not reached [end-of-life](https://duckdb.org/release_calendar), including LTS releases, and shows the 2 most recent patch releases of each. Older patch releases are not listed, but the extension may be available for them as well.
| Platform | 1.4.4 | 1.4.5 | 1.5.5 | 1.5.6 | 2.0.0 |
| :--- | :---: | :---: | :---: | :---: | :---: |
| Linux AMD64 | ✅ | ❌ | ✅ | ✅ | ✅ |
| Linux ARM64 | ✅ | ❌ | ✅ | ✅ | ✅ |
| macOS AMD64 | ✅ | ❌ | ❌ | ❌ | ❌ |
| macOS ARM64 | ✅ | ❌ | ✅ | ✅ | ✅ |
| Windows AMD64 | ❌ | ❌ | ❌ | ❌ | ❌ |
| Windows ARM64 | ❌ | ❌ | ❌ | ❌ | ❌ |
| WebAssembly | ❌ | ❌ | ✅ | ✅ | ✅ |
### Installing and Loading
```sql
INSTALL {{ page.extension.name }} FROM community;
LOAD {{ page.extension.name }};
```
{% if page.docs.hello_world %}
### Example
```sql
{{ page.docs.hello_world }}```
{% endif %}
{% if page.docs.extended_description %}
### About {{ page.extension.name }}
{{ page.docs.extended_description }}
{% endif %}
### Added Functions
| function_name | function_type | description | comment | examples |
|---------------------------------------|---------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------|-------------------------------------------------------------------------------------------------------------------|
| read_alignments | table | Read SAM/BAM alignment files as a table. Supports headerless SAM files with reference_lengths parameter, glob patterns, and parallel processing. | Also available as read_sam (alias) | [SELECT * FROM read_alignments('alignments.bam');] |
| read_fastx | table | Read FASTA/FASTQ sequence files as a table. Supports single-end and paired-end reads, glob patterns, gzip compression, and quality score offset conversion. | NULL | [SELECT * FROM read_fastx('reads.fastq.gz');] |
| read_sequences_sff | table | Read SFF (Standard Flowgram Format) files from 454/Roche sequencing. Returns read_fastx-compatible schema with optional quality/adapter trimming. | NULL | [SELECT * FROM read_sequences_sff('reads.sff');] |
| read_sequences_sam | table | Read sequences from SAM/BAM alignment files in read_fastx-compatible schema. Extracts sequence and quality data from alignments. | NULL | [SELECT * FROM read_sequences_sam('alignments.bam');] |
| read_biom | table | Read BIOM (Biological Observation Matrix) format files. Returns sparse COO format with sample_id, feature_id, and value columns. | HDF5-based BIOM v2.1 format | [SELECT * FROM read_biom('ogu_table.biom');] |
| read_gff | table_macro | Read GFF3 annotation files. Parses attributes column into a SQL MAP for easy querying. | Macro | [SELECT type, attributes['gene'] AS gene FROM read_gff('annotations.gff');] |
| read_ncbi | table | Fetch GenBank metadata from NCBI by accession number. Returns organism, length, taxonomy_id, and other metadata. | Requires httpfs extension | [SELECT * FROM read_ncbi('NC_000913.3');] |
| read_ncbi_fasta | table | Fetch FASTA sequences from NCBI by accession number. Returns data in read_fastx-compatible schema. | Requires httpfs extension | [SELECT * FROM read_ncbi_fasta('NC_000913.3');] |
| read_ncbi_annotation | table | Fetch feature annotations from NCBI by accession number. Returns data in read_gff-compatible schema. | Requires httpfs extension | [SELECT * FROM read_ncbi_annotation('NC_000913.3') WHERE type = 'gene';] |
| read_jplace | table_macro | Read jplace phylogenetic placement files. Returns best placement per fragment with edge_num, likelihood, and like_weight_ratio. | Macro - requires json extension | [SELECT fragment, edge_num, like_weight_ratio FROM read_jplace('placements.jplace');] |
| read_mzml | table | Read mzML mass spectrometry files. Returns one row per spectrum with metadata, m/z arrays, and intensity arrays. | NULL | [SELECT * FROM read_mzml('sample.mzML');] |
| read_mzxml | table | Read mzXML mass spectrometry files. Returns same schema as read_mzml for cross-format compatibility. | NULL | [SELECT * FROM read_mzxml('sample.mzXML');] |
| read_mzml_chromatograms | table | Read chromatogram data from mzML files. Returns chromatogram metadata with time and intensity arrays. | NULL | [SELECT * FROM read_mzml_chromatograms('sample.mzML');] |
| read_newick | table | Read Newick phylogenetic tree files. Returns one row per node with parent-child relationships and branch lengths. | NULL | [SELECT name, branch_length FROM read_newick('tree.nwk') WHERE is_tip;] |
| massql | table | Execute MassQL queries against mass spectrometry data. Supports conditions (MS1MZ, MS2PROD, MS2PREC, MS2NL), aggregations, and X/Y-variable pattern matching. | NULL | [SELECT * FROM massql('QUERY scaninfo(MS2DATA) WHERE MS2PROD=167.09', 'sample.mzML');] |
| align_minimap2 | table | Align query sequences to subject sequences using minimap2. Supports pre-built indexes for 10-30x performance improvement. | NULL | [SELECT * FROM align_minimap2('queries', subject_table='subjects');] |
| align_minimap2_sharded | table | Align query sequences against multiple pre-built minimap2 index shards in parallel. Reads are routed to specific shards via a mapping table. | NULL | [SELECT * FROM align_minimap2_sharded('queries', shard_directory='indexes/', read_to_shard='read_to_shard');] |
| save_minimap2_index | table | Build and save a minimap2 index to disk for reuse with align_minimap2. | NULL | [SELECT * FROM save_minimap2_index('subjects', 'refs.mmi', preset='sr');] |
| align_bowtie2 | table | Align query sequences to subject sequences using Bowtie2. Optimized for short reads. | Requires bowtie2 in PATH | [SELECT * FROM align_bowtie2('queries', 'subjects', preset='very-sensitive');] |
| align_bowtie2_sharded | table | Align query sequences against multiple pre-built Bowtie2 index shards in parallel. Reads are routed to specific shards via a mapping table. | Requires bowtie2 in PATH | [SELECT * FROM align_bowtie2_sharded('queries', shard_directory='indexes/', read_to_shard='read_to_shard');] |
| rype_classify | table | Classify sequences against a RYpe minimizer index. Returns bucket assignments with confidence scores. Supports paired-end and negative index filtering. | NULL | [SELECT * FROM rype_classify('index.ryxdi', 'seqs');] |
| rype_extract_minimizer_set | table | Extract deduplicated forward and reverse complement minimizer hash sets from sequences. | NULL | [SELECT * FROM rype_extract_minimizer_set('seqs', 32, 10);] |
| rype_extract_strand_minimizers | table | Extract minimizer hashes with positional information for both forward and reverse complement strands. | NULL | [SELECT * FROM rype_extract_strand_minimizers('seqs', 32, 10);] |
| rype_log_ratio | table | Compute log-ratio classification between two RYpe indices (numerator vs denominator). Returns per-read log-ratio scores. | NULL | [SELECT * FROM rype_log_ratio('numerator.ryxdi', 'denominator.ryxdi', 'seqs');] |
| alignment_is_paired | scalar | Test if read is paired (SAM flag 0x1). | Also available as is_paired | [SELECT * FROM read_alignments('a.bam') WHERE alignment_is_paired(flags);] |
| alignment_is_proper_pair | scalar | Test if read is properly paired (SAM flag 0x2). | Also available as is_proper_pair | [SELECT * FROM read_alignments('a.bam') WHERE alignment_is_proper_pair(flags);] |
| alignment_is_unmapped | scalar | Test if read is unmapped (SAM flag 0x4). | Also available as is_unmapped | [SELECT * FROM read_alignments('a.bam') WHERE NOT alignment_is_unmapped(flags);] |
| alignment_is_mate_unmapped | scalar | Test if mate is unmapped (SAM flag 0x8). | Also available as is_munmap | [SELECT * FROM read_alignments('a.bam') WHERE alignment_is_mate_unmapped(flags);] |
| alignment_is_reverse | scalar | Test if read is on reverse strand (SAM flag 0x10). | Also available as is_reverse | [SELECT * FROM read_alignments('a.bam') WHERE alignment_is_reverse(flags);] |
| alignment_is_mate_reverse | scalar | Test if mate is on reverse strand (SAM flag 0x20). | Also available as is_mreverse | [SELECT * FROM read_alignments('a.bam') WHERE alignment_is_mate_reverse(flags);] |
| alignment_is_read1 | scalar | Test if read is first in pair (SAM flag 0x40). | Also available as is_read1 | [SELECT * FROM read_alignments('a.bam') WHERE alignment_is_read1(flags);] |
| alignment_is_read2 | scalar | Test if read is second in pair (SAM flag 0x80). | Also available as is_read2 | [SELECT * FROM read_alignments('a.bam') WHERE alignment_is_read2(flags);] |
| alignment_is_secondary | scalar | Test if alignment is secondary (SAM flag 0x100). | Also available as is_secondary | [SELECT * FROM read_alignments('a.bam') WHERE NOT alignment_is_secondary(flags);] |
| alignment_is_primary | scalar | Test if alignment is primary (neither secondary nor supplementary). | NULL | [SELECT * FROM read_alignments('a.bam') WHERE alignment_is_primary(flags);] |
| alignment_is_qc_failed | scalar | Test if read failed QC (SAM flag 0x200). | Also available as is_qcfail | [SELECT * FROM read_alignments('a.bam') WHERE NOT alignment_is_qc_failed(flags);] |
| alignment_is_duplicate | scalar | Test if read is PCR/optical duplicate (SAM flag 0x400). | Also available as is_dup | [SELECT * FROM read_alignments('a.bam') WHERE NOT alignment_is_duplicate(flags);] |
| alignment_is_supplementary | scalar | Test if alignment is supplementary (SAM flag 0x800). | Also available as is_supplementary | [SELECT * FROM read_alignments('a.bam') WHERE NOT alignment_is_supplementary(flags);] |
| alignment_seq_identity | scalar | Calculate sequence identity between read and reference. Supports gap_compressed (default), gap_excluded, and blast methods. | NULL | [SELECT alignment_seq_identity(cigar, tag_nm, tag_md) FROM read_alignments('a.bam');] |
| sequence_dna_reverse_complement | scalar | Calculate reverse complement of DNA sequences. Supports IUPAC ambiguity codes and preserves case. | NULL | [SELECT sequence_dna_reverse_complement('ATCG');] |
| sequence_rna_reverse_complement | scalar | Calculate reverse complement of RNA sequences. Supports IUPAC ambiguity codes and preserves case. | NULL | [SELECT sequence_rna_reverse_complement('AUCG');] |
| sequence_dna_as_regexp | scalar | Convert DNA sequences with IUPAC codes to regular expression patterns for pattern matching. | NULL | [SELECT sequence_dna_as_regexp('ATNGG');] |
| sequence_rna_as_regexp | scalar | Convert RNA sequences with IUPAC codes to regular expression patterns for pattern matching. | NULL | [SELECT sequence_rna_as_regexp('AUNGG');] |
| formula | scalar | Compute monoisotopic mass in Daltons from a chemical formula string. | NULL | [SELECT formula('C6H12O6');] |
| massql_to_sql | scalar | Convert a MassQL query string to its generated SQL for debugging and inspection. | NULL | [SELECT massql_to_sql('QUERY scaninfo(MS2DATA) WHERE MS2PROD=167.09', 'sample.mzML');] |
| compress_intervals | aggregate | Aggregate function that merges overlapping genomic intervals into a minimal set of non-overlapping intervals. | NULL | [SELECT reference, compress_intervals(position, stop_position) FROM read_alignments('a.bam') GROUP BY reference;] |
| massdefect | macro | Compute the fractional mass (mass defect) of an m/z value. | Macro | [SELECT massdefect(100.0352);] |
| mz_within | macro | Check if observed m/z is within absolute tolerance (Da) of target m/z. | Macro | [SELECT mz_within(200.05, 200.0, 0.1);] |
| mz_within_ppm | macro | Check if observed m/z is within relative tolerance (ppm) of target m/z. | Macro | [SELECT mz_within_ppm(200.05, 200.0, 10);] |
| mz_massdefect_within | macro | Check if an m/z value's mass defect falls within a specified range. | Macro | [SELECT mz_massdefect_within(100.0352, 0.01, 0.05);] |
| mzml_peaks | table_macro | Unnest mz_array and intensity_array into per-peak rows with normalized intensities. | Macro - do not quote parameters | [SELECT * FROM mzml_peaks(spectra);] |
| mzml_scaninfo | table_macro | Re-aggregate peak-level data to one row per scan with summary statistics. | Macro - do not quote parameters | [SELECT * FROM mzml_scaninfo(peaks);] |
| mzml_scansum | table_macro | Compute total intensity per spectrum. | Macro - do not quote parameters | [SELECT * FROM mzml_scansum(peaks);] |
| mzml_scannum | table_macro | Return distinct spectrum indices. | Macro - do not quote parameters | [SELECT * FROM mzml_scannum(peaks);] |
| mzml_scanmz | table_macro | Return distinct precursor m/z values. | Macro - do not quote parameters | [SELECT * FROM mzml_scanmz(peaks);] |
| mzml_scanmaxint | table_macro | Return maximum intensity per spectrum. | Macro - do not quote parameters | [SELECT * FROM mzml_scanmaxint(peaks);] |
| mzml_ms1_peaks | table_macro | Filter mzml_peaks output to MS level 1 only. | Macro - do not quote parameters | [SELECT * FROM mzml_ms1_peaks(spectra);] |
| mzml_ms2_peaks | table_macro | Filter mzml_peaks output to MS level 2 only. | Macro - do not quote parameters | [SELECT * FROM mzml_ms2_peaks(spectra);] |
| mzml_ms1_parent_peaks | table_macro | Return MS1 peaks from parent scans of filtered MS2 peaks. | Macro - do not quote parameters | [SELECT * FROM mzml_ms1_parent_peaks(spectra, ms2_filtered);] |
| mzml_ms2_child_peaks | table_macro | Return MS2 peaks from child scans of filtered MS1 peaks. | Macro - do not quote parameters | [SELECT * FROM mzml_ms2_child_peaks(spectra, ms1_filtered);] |
| mzml_ms1_where_ms2prod | table_macro | MS1 peaks from parent scans of MS2 spectra containing a product ion at target m/z. | Macro - do not quote parameters | [SELECT * FROM mzml_ms1_where_ms2prod(spectra, 167.09);] |
| mzml_ms2_where_ms1mz | table_macro | MS2 peaks from child scans of MS1 spectra containing a peak at target m/z. | Macro - do not quote parameters | [SELECT * FROM mzml_ms2_where_ms1mz(spectra, 349.18);] |
| mzml_ms1_where_ms2prec | table_macro | MS1 peaks from parent scans of MS2 spectra with matching precursor m/z. | Macro - do not quote parameters | [SELECT * FROM mzml_ms1_where_ms2prec(spectra, 349.18);] |
| mzml_ms2_where_ms2prod_and_ms1mz | table_macro | MS2 peaks from scans with a product ion and whose parent MS1 has a peak at target m/z. | Macro - do not quote parameters | [SELECT * FROM mzml_ms2_where_ms2prod_and_ms1mz(spectra, 167.09, 349.18);] |
| mzml_filter_mz | table_macro | Filter peaks near a target m/z within tolerance. | Macro - do not quote parameters | [SELECT * FROM mzml_filter_mz(peaks, 167.09, 0.1);] |
| mzml_filter_nl | table_macro | Filter peaks with neutral loss near a target value within tolerance. | Macro - do not quote parameters | [SELECT * FROM mzml_filter_nl(peaks, 18.01, 0.1);] |
| mzml_excluded_ms2prod | table_macro | MS2 peaks from scans that do NOT contain a product ion at target m/z. | Macro - do not quote parameters | [SELECT * FROM mzml_excluded_ms2prod(spectra, 167.09);] |
| mzml_excluded_ms1mz | table_macro | MS1 peaks from scans that do NOT contain a peak at target m/z. | Macro - do not quote parameters | [SELECT * FROM mzml_excluded_ms1mz(spectra, 349.18);] |
| mzml_excluded_ms2prec | table_macro | MS2 peaks from scans whose precursor is NOT near target m/z. | Macro - do not quote parameters | [SELECT * FROM mzml_excluded_ms2prec(spectra, 349.18);] |
| mzml_x_offset_pair | table_macro | Find spectra with peaks at variable X and X+delta (pattern matching). | Macro - do not quote parameters | [SELECT * FROM mzml_x_offset_pair(spectra, 14.0);] |
| mzml_x_offset_triplet | table_macro | Find spectra with peaks at X, X+delta2, and X+delta3. | Macro - do not quote parameters | [SELECT * FROM mzml_x_offset_triplet(spectra, 14.0, 28.0);] |
| mzml_x_offset_ntuple | table_macro | Find spectra with peaks at X plus a list of N offsets. | Macro - do not quote parameters | [SELECT * FROM mzml_x_offset_ntuple(spectra, [14.0, 28.0, 42.0]);] |
| mzml_x_offset_pair_range | table_macro | Offset pair matching with X constrained to a min/max range. | Macro - do not quote parameters | [SELECT * FROM mzml_x_offset_pair_range(spectra, 14.0, 100.0, 500.0);] |
| mzml_x_prec_prod | table_macro | Find MS2 spectra where precursor minus delta matches a product ion. | Macro - do not quote parameters | [SELECT * FROM mzml_x_prec_prod(spectra, 18.01, 0.1, 5.0);] |
| mzml_x_prec_massdefect | table_macro | Find MS2 spectra with precursor mass defect in a specified range. | Macro - do not quote parameters | [SELECT * FROM mzml_x_prec_massdefect(spectra, 0.01, 0.05);] |
| mzml_x_ms1_ms2_prec | table_macro | Find MS2 spectra whose precursor matches an MS1 peak. | Macro - do not quote parameters | [SELECT * FROM mzml_x_ms1_ms2_prec(spectra);] |
| mzml_or_cardinality | table_macro | Match spectra containing N-of-M target m/z values (cardinality constraint). | Macro - do not quote parameters | [SELECT * FROM mzml_or_cardinality(spectra, [167.09, 181.10, 195.12], 0.1, 2, 3);] |
| mzml_peak_pair | table | Find peak pairs at X and 2*(X - formula_mass) for formula-based pattern matching. | Macro - do not quote parameters | [SELECT * FROM mzml_peak_pair(spectra, 'Fe');] |
| mzml_isotope_pattern | table_macro | Match spectra with isotope patterns at specified offsets and intensity ratios. | Macro - do not quote parameters | [SELECT * FROM mzml_isotope_pattern(spectra, [0.0, 1.003], [1.0, 0.5], [20.0, 20.0], 0.01);] |
| mzml_i_norm | macro | Max-normalize an intensity array by base peak intensity. | Macro | [SELECT mzml_i_norm(intensity_array, base_peak_intensity) FROM read_mzml('s.mzML');] |
| mzml_i_tic_norm | macro | TIC-normalize an intensity array by total ion current. | Macro | [SELECT mzml_i_tic_norm(intensity_array, total_ion_current) FROM read_mzml('s.mzML');] |
| parse_gff_attributes | macro | Parse a GFF3 attribute string (semicolon-delimited key=value pairs) into a DuckDB MAP. | Macro - helper for read_gff | [SELECT parse_gff_attributes('ID=gene1;Name=foo');] |
| woltka_ogu | table | Compute Woltka OGU counts over alignment data for a single sample. Accounts for multi-mapped reads. | Macro - do not quote parameters | [SELECT * FROM woltka_ogu(alignments, read_id);] |
| genome_coverage | table_macro | Compute genome coverage from alignment data. Compresses intervals per contig, maps to genomes, and returns proportion covered. | Macro - do not quote parameters | [SELECT * FROM genome_coverage(alignments, genome_lengths, contig_to_genome);] |
| bowtie2_available | scalar | Check if the bowtie2 binary is available in PATH. | Returns false in non-bowtie2 builds | [SELECT bowtie2_available();] |
| miint_version | scalar | Return the MIINT extension version string. | NULL | [SELECT miint_version();] |
| miint_versions | table | Return a table of dependency library versions (htslib, minimap2, WFA2-lib, etc.). | NULL | [SELECT * FROM miint_versions();] |
| align_pairwise_ksw2_score | scalar | NULL | NULL | NULL |
| align_sortmerna | table | NULL | NULL | NULL |
| bin_of | macro | NULL | NULL | NULL |
| circular_query_coverage | table_macro | NULL | NULL | NULL |
| cluster_upgma | table | NULL | NULL | NULL |
| ena_cancel | table | NULL | NULL | NULL |
| ks_2samp | scalar | NULL | NULL | NULL |
| trim_adapters_pe | scalar | NULL | NULL | NULL |
| absquant_orf_copies | table | NULL | NULL | NULL |
| align_abpoa | table | NULL | NULL | NULL |
| beta_knn | table_macro | NULL | NULL | NULL |
| bin_start | macro | NULL | NULL | NULL |
| cluster_kmeans | table | NULL | NULL | NULL |
| ena_modify_run | table | NULL | NULL | NULL |
| extract_linked_amplicon | scalar | NULL | NULL | NULL |
| install_gpl_boundary | scalar | NULL | NULL | NULL |
| interval_bins | macro | NULL | NULL | NULL |
| mask_dust | scalar | NULL | NULL | NULL |
| match_short_barcodes | table | NULL | NULL | NULL |
| cigar_query_coverage | scalar | NULL | NULL | NULL |
| detect_chimera_uchime_denovo | table | NULL | NULL | NULL |
| progressive_pcoa_from_unifrac | table | NULL | NULL | NULL |
| read_ncbi_lineage | table | NULL | NULL | NULL |
| trim_quality_5p | scalar | NULL | NULL | NULL |
| alignment_slice | table | NULL | NULL | NULL |
| compute_coverage_depth | aggregate | NULL | NULL | NULL |
| consensus_abpoa | table | NULL | NULL | NULL |
| ena_modify_experiment | table | NULL | NULL | NULL |
| pcoa | table | NULL | NULL | NULL |
| phylo_independent_contrasts | table | NULL | NULL | NULL |
| phylogeny_fasttree | table | NULL | NULL | NULL |
| read_alignment_header | table | NULL | NULL | NULL |
| align_pairwise_ksw2_cigar | scalar | NULL | NULL | NULL |
| align_pairwise_ksw2_dual_affine_full | scalar | NULL | NULL | NULL |
| align_pairwise_ksw2_splice_score | scalar | NULL | NULL | NULL |
| infer_trim | table_macro | NULL | NULL | NULL |
| is_unmapped | scalar | NULL | NULL | NULL |
| miint_warnings | table_macro | NULL | NULL | NULL |
| phylo_ancestral_parsimony | table | NULL | NULL | NULL |
| read_ena_sequences | table | NULL | NULL | NULL |
| trim_adapters | scalar | NULL | NULL | NULL |
| align_pairwise_ksw2_dual_affine_cigar | scalar | NULL | NULL | NULL |
| cigar_query_intervals | scalar | NULL | NULL | NULL |
| cigar_sequence_identity | scalar | NULL | NULL | NULL |
| ena_modify_sample | table | NULL | NULL | NULL |
| genome_coverage_per_sample | table_macro | NULL | NULL | NULL |
| mmvec_fit | table | NULL | NULL | NULL |
| phylo_ancestral_states | table | NULL | NULL | NULL |
| alignment_is_mapped_primary | scalar | NULL | NULL | NULL |
| ena_searchable_fields | table | NULL | NULL | NULL |
| is_reverse | scalar | NULL | NULL | NULL |
| permanova | table | NULL | NULL | NULL |
| simulate_gradient_otus | table | NULL | NULL | NULL |
| cumulative_coverage | aggregate | NULL | NULL | NULL |
| is_dup | scalar | NULL | NULL | NULL |
| mmvec_ranks | table | NULL | NULL | NULL |
| place_krepp | table | NULL | NULL | NULL |
| read_ncbi_taxdump | table | NULL | NULL | NULL |
| search_sequences_vsearch | table | NULL | NULL | NULL |
| trim_polyx | scalar | NULL | NULL | NULL |
| _miint_bin_index | macro | NULL | NULL | NULL |
| align_pairwise_ksw2_full | scalar | NULL | NULL | NULL |
| align_pairwise_wfa2_cigar | scalar | NULL | NULL | NULL |
| cigar_pooled_identity | aggregate | NULL | NULL | NULL |
| ena_upload_reads | table | NULL | NULL | NULL |
| is_qcfail | scalar | NULL | NULL | NULL |
| is_read1 | scalar | NULL | NULL | NULL |
| is_read2 | scalar | NULL | NULL | NULL |
| shear_tree | table | NULL | NULL | NULL |
| beta_knn_from_sample | table_macro | NULL | NULL | NULL |
| blast | table | NULL | NULL | NULL |
| ena_hold | table | NULL | NULL | NULL |
| ena_release | table | NULL | NULL | NULL |
| is_secondary | scalar | NULL | NULL | NULL |
| krepp_index_create | table | NULL | NULL | NULL |
| pick_anchors | table | NULL | NULL | NULL |
| read_ena_attributes | table | NULL | NULL | NULL |
| read_jplace_newick | table | NULL | NULL | NULL |
| save_bowtie2_index | table | NULL | NULL | NULL |
| simulate_cluster_otus | table | NULL | NULL | NULL |
| sylph_index_create | table | NULL | NULL | NULL |
| tree_resolve_multifurcations | table | NULL | NULL | NULL |
| trim_quality_sliding | scalar | NULL | NULL | NULL |
| unifrac_permanova | table | NULL | NULL | NULL |
| ena_modify_project | table | NULL | NULL | NULL |
| merge_pairs_vsearch | scalar | NULL | NULL | NULL |
| taxonomy_lineage | table_macro | NULL | NULL | NULL |
| trim_polyg | scalar | NULL | NULL | NULL |
| absquant_fit_models | table | NULL | NULL | NULL |
| cluster_sequences_vsearch | table | NULL | NULL | NULL |
| community_distances | table | NULL | NULL | NULL |
| compute_msa_consensus | aggregate | NULL | NULL | NULL |
| cumulative_coverage_curve | table_macro | NULL | NULL | NULL |
| detect_chimera_uchime | table | NULL | NULL | NULL |
| filter_read | scalar | NULL | NULL | NULL |
| is_mreverse | scalar | NULL | NULL | NULL |
| is_munmap | scalar | NULL | NULL | NULL |
| mmvec_predict | table | NULL | NULL | NULL |
| phylogeny_fasttree_available | scalar | NULL | NULL | NULL |
| progressive_pcoa_from_distances | table | NULL | NULL | NULL |
| read_sam | table | NULL | NULL | NULL |
| tree_resolve_placement | table | NULL | NULL | NULL |
| absquant_cell_counts | table | NULL | NULL | NULL |
| align_pairwise_ksw2_dual_affine_score | scalar | NULL | NULL | NULL |
| cigar_query_length | scalar | NULL | NULL | NULL |
| compute_pileup | table | NULL | NULL | NULL |
| procrustes | table | NULL | NULL | NULL |
| read_ncbi_taxdump_deleted | table | NULL | NULL | NULL |
| read_ncbi_taxdump_merged | table | NULL | NULL | NULL |
| region_presence | table_macro | NULL | NULL | NULL |
| trim_quality_3p | scalar | NULL | NULL | NULL |
| unifrac_pcoa | table | NULL | NULL | NULL |
| align_mafft | table | NULL | NULL | NULL |
| is_supplementary | scalar | NULL | NULL | NULL |
| mmvec_score | table | NULL | NULL | NULL |
| read_ncbi_taxdump_names | table | NULL | NULL | NULL |
| region_coverage | table_macro | NULL | NULL | NULL |
| align_pairwise_ksw2_splice_cigar | scalar | NULL | NULL | NULL |
| align_pairwise_wfa2_full | scalar | NULL | NULL | NULL |
| beta_group_distances | table_macro | NULL | NULL | NULL |
| mmvec_train_test_split | table_macro | NULL | NULL | NULL |
| progressive_pcoa_from_features | table | NULL | NULL | NULL |
| qc_version | scalar | NULL | NULL | NULL |
| read_ena | table | NULL | NULL | NULL |
| unifrac_distances | table | NULL | NULL | NULL |
| unifrac_faith_pd | table | NULL | NULL | NULL |
| align_pairwise_ksw2_splice_full | scalar | NULL | NULL | NULL |
| align_pairwise_wfa2_score | scalar | NULL | NULL | NULL |
| align_sortmerna_rrna | table | NULL | NULL | NULL |
| deblur | table | NULL | NULL | NULL |
| is_paired | scalar | NULL | NULL | NULL |
| is_proper_pair | scalar | NULL | NULL | NULL |
| phylo_ancestral_ml | table | NULL | NULL | NULL |
| rarefy_feature_table | table | NULL | NULL | NULL |
| rype_index_create | table | NULL | NULL | NULL |
| sequence_split | scalar | NULL | NULL | NULL |
| sylph_profile | table | NULL | NULL | NULL |
### Overloaded Functions
This extension does not add any function overloads.
### Added Types
This extension does not add any types.
### Added Settings
| name | description | input_type | scope | aliases | typed_value |
|------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|--------|---------|-------------|
| miint_ena_validate_only | When true, the next INSERT INTO ena.* is sent as a Webin V2 VALIDATE (server-side dry-run) instead of ADD. No accessions are returned. Default false. | BOOLEAN | GLOBAL | [] | false |
| miint_rype_arrow_batch_bytes | Byte ceiling on one Arrow record batch's sequence payload in rype_classify / rype_log_ratio / rype_extract_*. 0 disables the ceiling, restoring a single unbounded batch. Default 256 MiB. | BIGINT | GLOBAL | [] | 268435456 |
| temp_directory | Set the directory to which temporary files are written. | VARCHAR | GLOBAL | [] | post.db.tmp |