# Output

### gene_presence_absence.csv

A csv file describing which gene is in which sample. If a gene cluster is present in a sample, the sequence name of the representative for that sample is given in the matrix. The corresponding DNA and protein sequence can then be matched to those found in the `combined_DNA_CDS.fasta` and `combined_protein_CDS.fasta` files. The format is the same as that given by [Roary](https://sanger-pathogens.github.io/Roary/).

Annotations that have been merged will be separated by a semicolon. Refound genes that include a stop codon will have '_stop' appended to the end of the gene name. This indicates they could be a potential pseudo gene. Gene within a cluster that have an unusual length will have '_len' appended to the gene name.

### gene_presence_absence.Rtab

A binary tab separated version of the `gene_presence_absence.csv` file describing which gene is in which sample. The format is the same as that given by [Roary](https://sanger-pathogens.github.io/Roary/).

### final_graph.gml

The final pan-genome graph generated by Panaroo. This can be viewed easily using Cytoscape (see [Visualising the Pangenome](vis/cytoscape.md) for more details). It includes all the meta-information such as gene annotation and which gene/edge is present in which genome. It can also be loaded into python using networkx for further processing.

### struct_presence_absence.csv

A csv file which lists the presence and absence of different genomic rearrangement events. The genes involved in each event are listed in the respective column names of the csv. The thresholds for calling these events can be changed by adjusting the `--min_edge_support_sv` parameter when calling Panaroo.

### pan_genome_reference.fa

This is a similar output to that produced by [Roary](https://sanger-pathogens.github.io/Roary/). It creates a linear reference genome of all the genes found in the dataset. The order of the genes in this reference are not significant. NOTE: to avoid issues with the multi-mapping of reads, paralogous gene clusters will only be represented once in this reference.

### gene_data.csv

This is a very large file mainly used internally in the program. It links each gene sequence and annotation to the internal representations used. It can be useful in interpreting some of the output especially the 'final_graph.gml' file.

### combined_DNA_CDS.fasta

This is a fasta file which includes all nucleotide sequence for both the annotated genes and those refound by the program. The gene names are the internal ones used by Panaroo. These can be translated to the original names using the 'gene_data.csv' file.

### combined_protein_CDS.fasta

Similar to the `combined_DNA_CDS.fasta` file, this is a fasta file which includes all protein sequence for both the annotated genes and those refound by the program. The gene names are the internal ones used by Panaroo. These can be translated to the original names using the 'gene_data.csv' file.

### core_gene_alignment.aln

An alignment of genes present in at least the fraction of genomes specified by the `--core_threshold` parameter (default=0.95). Currently, in cases where a gene is fragmented only the longer fragment will appear in this output.

### core_gene_alignment_filtered.aln

This alignment is recommended for building core genome phylogenies. It is a filtered version of the core genome alignment. Additional genes are removed if they exceed the Block Mapping and Gathering with Entropy (BMGE) filter. This is set using the `--core_entropy_filter` parameter. By default this automatically adapts to each dataset and identifies outlying genes using Tukey's outlier test (recommended).