New: binned coverage plot option in reports.py align_and_plot via --binLargePlots (#957) (thanks to @lakras) metagenomics.py taxlevel_summary can now also aggregate reports in KrakenUniq format (#948) krakenuniq WDL task (and demux_plus, etc.) writes a viral summary tsv, aggregating kraken reports from all input samples (#948) add aggregate_spike_count function to reports.py to write a tsv table of spike-ins seen in all samples, aggregating separate spike-in reports (#955, #973, #981) an optional QC check has been added to taxon_filter.py filter_lastal_bam (#961) raises a QCError() if the sample name (bam file basename) begins with any number of negative control prefixes ("neg", "water", "NTC") and lastal has identified reads to keep after...
What's Changed new features turn on allowNestedInputs for subworkflows: this exposes to the end-use...
A set of scripts and tools for the analysis of viral NGS data. More detailed documentation can be f...
New: [#762] The taxon_filter.py file now has a new command, deplete_bwa_bam, which uses bwa for dep...
New: binned coverage plot option in reports.py align_and_plot via --binLargePlots (#957) (thanks to...
This is a release with many changes, including new WDL pipelines, a distribution of viral-ngs on DNA...
New: WDL workflow for Genbank submission [#797, #793, #800] metagenomics.py taxlevel_summary to tab...
A set of scripts and tools for the analysis of viral NGS data. More detailed documentation can be f...
New: WDL workflow added to read_utils.wdl::downsample() [#819, #821, #823] WDL workflows added for ...
New: The Snakemake pipeline can now source database files from S3, GS, or SFTP if given protocol-pr...
new features: new workflow sarscov2_nextstrain [#204, #208, #219] updates to genbank submission [#2...
New: Improvements to the pipeline to support single-end reads in additional stages, including the d...
New: The functions to plot coverage in reports.py can now limit graph bounds via --plotXLimits and ...
New: The Snakemake pipeline can now source database files from S3, GS, or SFTP if given protocol-pr...
New: New BWA-based LCA metagenomics function: metagenomics. align_rna() Align to metagenomics bwa i...
New: scaffolder uses ambiguous alignments when no unambiguous ones exist (#904) add function to ass...
What's Changed new features turn on allowNestedInputs for subworkflows: this exposes to the end-use...
A set of scripts and tools for the analysis of viral NGS data. More detailed documentation can be f...
New: [#762] The taxon_filter.py file now has a new command, deplete_bwa_bam, which uses bwa for dep...
New: binned coverage plot option in reports.py align_and_plot via --binLargePlots (#957) (thanks to...
This is a release with many changes, including new WDL pipelines, a distribution of viral-ngs on DNA...
New: WDL workflow for Genbank submission [#797, #793, #800] metagenomics.py taxlevel_summary to tab...
A set of scripts and tools for the analysis of viral NGS data. More detailed documentation can be f...
New: WDL workflow added to read_utils.wdl::downsample() [#819, #821, #823] WDL workflows added for ...
New: The Snakemake pipeline can now source database files from S3, GS, or SFTP if given protocol-pr...
new features: new workflow sarscov2_nextstrain [#204, #208, #219] updates to genbank submission [#2...
New: Improvements to the pipeline to support single-end reads in additional stages, including the d...
New: The functions to plot coverage in reports.py can now limit graph bounds via --plotXLimits and ...
New: The Snakemake pipeline can now source database files from S3, GS, or SFTP if given protocol-pr...
New: New BWA-based LCA metagenomics function: metagenomics. align_rna() Align to metagenomics bwa i...
New: scaffolder uses ambiguous alignments when no unambiguous ones exist (#904) add function to ass...
What's Changed new features turn on allowNestedInputs for subworkflows: this exposes to the end-use...
A set of scripts and tools for the analysis of viral NGS data. More detailed documentation can be f...
New: [#762] The taxon_filter.py file now has a new command, deplete_bwa_bam, which uses bwa for dep...