New: Changed: in WDL workflows, default demultiplexing parameters to support novaseq [#868] in illumina.py::illumina_demux: max_mismatches changed 0 -> 1, and minimum_base_quality: 25 -> 10 This supports the four Q scores written by the Novaseq Upgraded: samtools (and htslib) 1.7 -> 1.9 [#870] pysam 0.14.1 -> 0.15.0 [#870] picard 2.18.9 -> 2.18.11 [#869
New: binned coverage plot option in reports.py align_and_plot via --binLargePlots (#957) (thanks to...
Changed: Improved HiSeq X / HiSeq 4000 compatibility: broken symlinks are now removed from Illumina...
New: New BWA-based LCA metagenomics function: metagenomics. align_rna() Align to metagenomics bwa i...
New: WDL workflow added to read_utils.wdl::downsample() [#819, #821, #823] WDL workflows added for ...
Changed: improve handling of possible feature table IDs [#846] Fixed: genome feature annotation t...
New: scaffolder uses ambiguous alignments when no unambiguous ones exist (#904) add function to ass...
New: illumina.common_barcodes now reports Illumina index names in addition to barcode sequences. Ex...
Fixed: fix position output for genome features falling oob during annotation in snakemake pipeline:...
A set of scripts and tools for the analysis of viral NGS data. More detailed documentation can be f...
This is a release with many changes, including new WDL pipelines, a distribution of viral-ngs on DNA...
Changed: Demultiplexing from Illumina basecalls is now more permissive of varying input directory [...
New: The functions to plot coverage in reports.py can now limit graph bounds via --plotXLimits and ...
Fixed: CheckIlluminaDirectory now creates symlinks only if necessary Fix plot_coverage for cases wh...
New: illumina.py illumina_demux now supports simplex runs: non-multiplexed flowcells that do not ha...
New or changed WDL workflows: new workflow: subsample_by_metadata_with_focal [#161] Changes: rena...
New: binned coverage plot option in reports.py align_and_plot via --binLargePlots (#957) (thanks to...
Changed: Improved HiSeq X / HiSeq 4000 compatibility: broken symlinks are now removed from Illumina...
New: New BWA-based LCA metagenomics function: metagenomics. align_rna() Align to metagenomics bwa i...
New: WDL workflow added to read_utils.wdl::downsample() [#819, #821, #823] WDL workflows added for ...
Changed: improve handling of possible feature table IDs [#846] Fixed: genome feature annotation t...
New: scaffolder uses ambiguous alignments when no unambiguous ones exist (#904) add function to ass...
New: illumina.common_barcodes now reports Illumina index names in addition to barcode sequences. Ex...
Fixed: fix position output for genome features falling oob during annotation in snakemake pipeline:...
A set of scripts and tools for the analysis of viral NGS data. More detailed documentation can be f...
This is a release with many changes, including new WDL pipelines, a distribution of viral-ngs on DNA...
Changed: Demultiplexing from Illumina basecalls is now more permissive of varying input directory [...
New: The functions to plot coverage in reports.py can now limit graph bounds via --plotXLimits and ...
Fixed: CheckIlluminaDirectory now creates symlinks only if necessary Fix plot_coverage for cases wh...
New: illumina.py illumina_demux now supports simplex runs: non-multiplexed flowcells that do not ha...
New or changed WDL workflows: new workflow: subsample_by_metadata_with_focal [#161] Changes: rena...
New: binned coverage plot option in reports.py align_and_plot via --binLargePlots (#957) (thanks to...
Changed: Improved HiSeq X / HiSeq 4000 compatibility: broken symlinks are now removed from Illumina...
New: New BWA-based LCA metagenomics function: metagenomics. align_rna() Align to metagenomics bwa i...