Release notes for FastQ Screen v0.16.0 (20 September 2024) ---------------------------------------------------------- Added functionality to process long sequence reads by using Minimap2 as the aligner. We would like to thank Martin Pollard (Wellcome Sanger Institute, UK) for contributing this improvement. Release notes for FastQ Screen v0.15.3 (03 April 2023) ------------------------------------------------------ Fixed filtering bug causing the final filtered FASTQ file to have the file extension .fastq when it should be .fastq.gz, since the file is actually gzipped. Release notes for FastQ Screen v0.15.2 (26 January 2022) -------------------------------------------------------- Updated documentation Provided details on the genomes downloaded with the command --get_genomes for possible future reference. Release notes for FastQ Screen v0.15.1 (11 January 2022) -------------------------------------------------------- Updated contact details. Release notes for FastQ Screen v0.14.1 (03 June 2020) ---------------------------------------------------------- Added --score_min L,0,-0.6 as a Bismark/Bowtie2 mapping parameter to make FastQ Screen perform less stringent mapping, which is more consistent with non-bisulfite FastQ Screen mapping. Added a GitHUb Actions YAML file for testing FastQ Screen. Release notes for FastQ Screen v0.14.0 (17 June 2019) ---------------------------------------------------------- New --add_genome option. Fixed bug causing FastQ Screen to run when aligner not present. Release notes for FastQ Screen v0.13.0 (12 September 2018) ---------------------------------------------------------- Added --get_genomes option. Updated documentation. Release notes for FastQ Screen v0.12.2 (16 August 2018) ------------------------------------------------------- For bisulfite mapping, bismark is now run in --ambiguous mode to identify multi-mapping reads. Release notes for FastQ Screen v0.12.1 (24 July 2018) ----------------------------------------------------- Added --inverse option for filtering files. Improved results display format. Release notes for FastQ Screen v0.12.0 (15 June 2018) ----------------------------------------------------- Interactive HTML graphs now made using Plotly. Release notes for FastQ Screen v0.11.4 (27 November 2017) --------------------------------------------------------- FASTQ files are edited so that the third line of a read is always a plus symbol. This prevents tagged/filtered output files not technically adhering to FASTQ format. Release notes for FastQ Screen v0.11.3 (16 October 2017) -------------------------------------------------------- FastQ Screen uses full path to dependencies rather than Bowtie, Bowtie2 etc. Release notes for FastQ Screen v0.11.2 (21 September 2017) ---------------------------------------------------------- Fixed bug preventing --tag being selected without --filter. In bisulfite mode, FastQ Screen no longer assumes that Bowtie/Bowtie2 are always in the path (even if specified otherwise in the config file). FastQ Screen now terminates before creating a subset file if no aligner/Bismark executable file is found. FastQ Screen no longer gives an initialisation warning if, in the configuration file, the DATABASE line does not specify a database name and/or database path. Release notes for FastQ Screen v0.11.1 (23 February 2017) --------------------------------------------------------- v0.11.1 is a minor release. Fixed bug preventing user selecting --filter option 4 or 5. Release notes for FastQ Screen v0.11.0 (22 February 2017) --------------------------------------------------------- v0.11.0 is a major release. Added --filter options 4 and 5. Added option --pass to further improve filtering. Prevented HTML bar graphs overlapping when screening against multiple genomes. Corrected documentation describing how to use the option --top. Release notes for FastQ Screen v0.10.0 (19 January 2017) ----------------------------------------------------------- v0.10.0 is a major release. Added --top functionality for when faster processing times is the main priority. Improved presentation of HTML graphs. Release notes for FastQ Screen v0.9.5 (07 December 2016) -------------------------------------------------------- v0.9.5 is a minor release. Fixed bug causing FastQ Screen, when running in --bisulfite mode, to mislabel species names in the HTML bisulfite read orientation graph on the occasion that one or more of the samples tested contained reads that mapped to none of the bisulfite converted reference genomes. Release notes for FastQ Screen v0.9.4 (21 November 2016) -------------------------------------------------------- v0.9.4 is a minor release. New colour scheme which should be easily interpretable by colour blind people. Fixed bug preventing, in some instances, genome names being displayed in the header line of filtered (using the --filter option) FASTQ files. Release notes for FastQ Screen v0.9.3 (31 October 2016) ------------------------------------------------------- v0.9.3 is a minor release. Fixed bug stopping the command-line --threads option overriding the configuration file. When the --tag option was specified, FastQ Screen should have analysed all the reads in a file by default. However, a bug resulted in a subset file being generated and analysed instead. This has been fixed and now a reduced reads file will only be generated with the --tag option if explicitly requested using the --subset command. Fixed bug causing FastQ Screen to not process reads containing a full-stop in the FASTQ read header. Changes to what is reported when using the --quiet option Updated documentation. Release notes for FastQ Screen v0.9.2 (12 October 2016) ------------------------------------------------------- v0.9.2 is a minor release. When --outdir option selected, FastQ Screen creates the output directory if it does not already exist. FastQ Screen in bisulfite mode checks whether the bisulfite orientation graph already exists. Adjusted how compressed files are read to improve compatibility with Mac systems. Fixed bug causing the HTML report to be missing one genome when reporting conventional (i.e. not bisulfite) alignment results Updated documentation. Release notes for FastQ Screen v0.9.1 (05 October 2016) ------------------------------------------------------- v0.9.1 is a minor release. Fixed bug causing FastQ Screen to terminate prematurely when in bisulfite mode if no reads map to a bisulfite reference genome. Release notes for FastQ Screen v0.9.0 (04 October 2016) ------------------------------------------------------- v0.9.0 is a major release. FastQ Screen, when run in Bisulfite mode, reports to which strand reads aligned (original top strand, complementary to original top strand, complementary to original bottom strand, or original bottom strand). Release notes for FastQ Screen v0.8.0 (08 September 2016) --------------------------------------------------------- v0.8.0 is a major release. Program is now compatible with aligner BWA FastQ Screen produces an HTML summary report Program documentation has been substantially updated and is now in Markdown format Release notes for FastQ Screen v0.7.0 (01 August 2016) ------------------------------------------------------ v0.7.0 is a major release. Added --tag option to create output FASTQ files in which the the genomes to which a read maps is appended to the first line of the FASTQ read. Added --filter option to extract reads from a tagged FASTQ file which map, or do not map, to a specified combination of genomes. Pre-existing option --nohits is now equivalent to the parameters --tag --filter 000 (number of zeroes corresponds to the number of genome being screened) Release notes for FastQ Screen v0.6.4 (12 July 2016) ---------------------------------------------------- v0.6.4 is a minor release. Program no longer terminates if a single Bismark reference genome index is incorrectly specified. Fixed bug causing program to crash if --aligner bowtie2 and --bisulfite specified together. FastQ Screen can now use Bowtie (in addition to Bowtie2) when performing Bisulfite mapping with Bismark. Fixed bug in how FastQ Screen checks for dependencies (e.g. SamTools). Release notes for FastQ Screen v0.6.3 (07 July 2016) ---------------------------------------------------- v0.6.3 is a minor release. Fixed bug causing --subset 0 to crash. Fixed bug in which the reported percentage reads mapping to no libraries was, in some instances, an underestimate of the correct value. Release notes for FastQ Screen v0.6.2 (05 July 2016) ---------------------------------------------------- v0.6.2 is a minor release. Updated help text. Refactored code. Release notes for FastQ Screen v0.6.1 (01 July 2016) ---------------------------------------------------- v0.6.1 is a minor release. Fixed bug causing program to crash in some instances when --outdir option selected. Release notes for FastQ Screen v0.6.0 (27 June 2016) ---------------------------------------------------- v0.6.0 is a major release. Compatible with Bismark, enabling bisulfite library QC. Use the option --bisulfite when processing bisulfite libraries. The path to Bismark may be specified in the configuration file. Bisulfite libraries cannot be processed simultaneously with non-bisulfite libraries. Bismark can be downloaded from: www.bioinformatics.babraham.ac.uk/projects/bismark Option --colorspace is no longer supported. Release notes for FastQ Screen v0.5.2 (07 September 2015) --------------------------------------------------------- v0.5.2 is a minor release. Fixed bug observed when --nohits option selected causing initialization warnings, in some instances. Release notes for FastQ Screen v0.5.1 (14 July 2015) ---------------------------------------------------- v0.5.1 is a minor release. Program checks the configuration to ensure a FASTQ file is not mapped against the same library more than once. Release notes for FastQ Screen v0.5.0 (29 June 2015) ---------------------------------------------------- v0.5.0 is a major release. Please note that users no longer need to specify whether a genome index is compatible with bowtie or bowtie2, since this is now determined automatically. Option --subset 100000 is now the default. Use --subset 0 to process an entire file (not recommended for most QC applications, since this generally takes much more time). Option --paired removed. Mapping forward or reverse reads independently should be adequate to ascertain whether there is contamination, and will also provide the user with additional information if the forward reads are more prone generally to contamination than the reverse reads (or vice versa). Also, sometimes the script will fail to detect contamination in --paired mode. For example, if the read pair did not constitute a contiguous region of DNA, or if the paired reads were separated by are large distance (such as RNA seq). Bowtie2 is now the default aligner, replacing the orignal bowtie. New option --force instructs FastQ Screen to overwrite extant output files. The script now uses a more memory efficient internal data structure for recording which reads map to what library. However, this means that a maximum of 15 libraries may be specified with 32-bit Perl or 31 libraries with 64-bit Perl. Release notes for FastQ Screen v0.4.4 ------------------------------------- v0.4.4 is a minor release. Fixed a bug in the code which checked for the presence of bowtie2 indices for large genomes. Added a nicer font for the graph and improved some of the colours Fixed the output file naming for .fq files and files with names ending in .gz. Release notes for FastQ Screen v0.4.3 ------------------------------------- v0.4.3 is a minor release. Fixed bug causing all reads to be written to the 'no hits' output file when using Bowtie2 as the aligner. Bowtie2 now runs with the parameters '--no-discordant' and '--no-mixed' when mapping paired-end reads. The 'nohits' output file has the file extension '.fastq' and is compressed if the input files are compressed. Release notes for FastQ Screen v0.4.2 ------------------------------------- v0.4.2 is a minor release. The script no longer defaults to Bowtie if "--aligner" is not specified. Instead, the script checks the configuration file to determine if Bowtie/Bowtie2 paths and indices have been specified. If both Bowtie and Bowtie2 indices have been specified, FastqScreen then defaults to the original Bowtie. The script now reports the number of reads mapping each genome in addition to percentages. Release notes for FastQ Screen v0.4.1 ------------------------------------- v0.4.1 is a minor release. A new command line argument has been introduced (--aligner, -a) which enables the user to select the sequence aligner to use; valid options are 'bowtie' (default) or 'bowtie2'. Fastq_screen now only uses one aligner per round of screening and so if the configuration file lists paths to both bowtie and bowtie2 libraries, only the libraries for the specified aligner will be imported. Other changes: * The script will skip the production of graphs if GD::Graph is not installed to prevent terminating in error. * Standard error is now reported as a separate file for each library. Release notes for FastQ Screen v0.4 ----------------------------------- v0.4 is a major release enabling FastQ Screen to use Bowtie2 as the sequence aligner. Bowtie2 may be preferred since it is more efficient than its predecessor at processing longer reads and can perform gapped alignments. The configuration file instructs FastQ Screen as to which aligner to use. We would like to thank Patrick J Biggs (Institute of Veterinary, Animal & Biomedical Sciences, Massey University, New Zealand) and Saulo Alves Aflitos (Plant Research International, Wageningen, The Netherlands) for suggesting this improvement. Release notes for FastQ Screen v0.3.1 ------------------------------------- v0.3.1 is a minor release fixing a bug that prevented the script receiving options using the Bowtie argument (--bowtie, -b). Release notes for FastQ Screen v0.3 ----------------------------------- v0.3 has new data analysis, output and file handling functionality. The most significant change is the removal of the multilib option. The script now calculates the percentage of sequences that map: i) uniquely to the specified genome but no others; ii) more than once to the specified genome but to no others; iii) once to the specified genome and to other libraries; iv) more than once to the specified genome and other libraries as well; iv) to none of the reference genomes. Essentially, this combines the functionality of selecting/not selecting multilib in the previous version of FastQ Screen. Other changes: * A new option (--nohits) prints to an output file sequence reads or read pairs that mapped to none of the reference genomes. If used in conjunction with the subset option, only reads/read pairs present in the temporary subset file that failed to map to any genome will be returned. * The script can now process zipped FASTQ files with the file extension 'gz'. * The --illumina flag has changed to --illumina1_3 in recognition of current Illumina sequencers now reporting in Sanger format. * The script can now process files with names that contain spaces. Release notes for FastQ Screen v0.2.1 ------------------------------------- v0.2.1 is a minor release which fixes a bug in paired end multilib searches where the mapped percentage values reported are double the true values (leading to percentages >100% and corrupted graphs). Single end searches and searches using the default mode (rather than multilib) were unaffected. Release notes for FastQ Screen v0.2 ----------------------------------- v0.2 adds some new features and a new mode of analysis. The major change is a new way of analysing data called multilib mode. This mode is activated by passing the --multilib argument to the program on the command line. In this mode each individual sequence searched is tracked across all search libraries. The single and multiple hits in the output therefore say how many sequences hit this, and only this, library, and how many hit this library and one or more other libraries. In multilib mode it doesn't matter how many times a sequence could have been mapped in a given library, only whether it found a hit or not. Because multilib mode needs to record the pattern of hits for every single sequence searched it will have significantly higher memory usage than the default search mode, especially if run without the --subset option enabled. Other changes in this release are: * The addition of colorspace support via the --color option. To use this option your bowtie indices will need to have been generated with the colorspace flag set. * A new option (--conf) to manually specify a location for the config file rather than using the default file installed with the program. Makes it easy to switch between different sets of libraries. * A new option (--threads) to override the default setting in the conf file for how many threads to parallelise your searches across.