Bug fixes, tested support for multi-segment genomes, and ability to download FASTAs, feature tables, and full GenBank records via the Entrez REST API. Integration of these features into the Snakemake rules and config.json. PEP8 formatting. RTD documentation
New: Improvements to the pipeline to support single-end reads in additional stages, including the d...
Implementation of basic metagenomics tools: kraken and krona. Bug fix for silent tool failures intro...
Bugfixes and unit testing of Trinity and fixes to Broad-specific pipeline scripts
Move software dependencies to bioconda for greater reliability / cross-platform compatibility. Code ...
Updates: make easy-deploy script more generic (less Broad specific) more documentation updates bug...
New: The Snakemake pipeline can now source database files from S3, GS, or SFTP if given protocol-pr...
Robust behavior in depletion, assembly and metagenomics for empty or almost-empty data sets. More in...
New: The Snakemake pipeline can now source database files from S3, GS, or SFTP if given protocol-pr...
Tune nucmer parameters in scaffolding step to tolerate more diverse viruses (HIV, Influenza). Misc b...
Fixed: fix position output for genome features falling oob during annotation in snakemake pipeline:...
Bugfixes with multi-segment genomes where the reference sequence names are not in alpha order. Impro...
An analysis package for viral sequence data. Includes read processing (human depletion, etc), de no...
New: New BWA-based LCA metagenomics function: metagenomics. align_rna() Align to metagenomics bwa i...
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...
New: Improvements to the pipeline to support single-end reads in additional stages, including the d...
Implementation of basic metagenomics tools: kraken and krona. Bug fix for silent tool failures intro...
Bugfixes and unit testing of Trinity and fixes to Broad-specific pipeline scripts
Move software dependencies to bioconda for greater reliability / cross-platform compatibility. Code ...
Updates: make easy-deploy script more generic (less Broad specific) more documentation updates bug...
New: The Snakemake pipeline can now source database files from S3, GS, or SFTP if given protocol-pr...
Robust behavior in depletion, assembly and metagenomics for empty or almost-empty data sets. More in...
New: The Snakemake pipeline can now source database files from S3, GS, or SFTP if given protocol-pr...
Tune nucmer parameters in scaffolding step to tolerate more diverse viruses (HIV, Influenza). Misc b...
Fixed: fix position output for genome features falling oob during annotation in snakemake pipeline:...
Bugfixes with multi-segment genomes where the reference sequence names are not in alpha order. Impro...
An analysis package for viral sequence data. Includes read processing (human depletion, etc), de no...
New: New BWA-based LCA metagenomics function: metagenomics. align_rna() Align to metagenomics bwa i...
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...
New: Improvements to the pipeline to support single-end reads in additional stages, including the d...
Implementation of basic metagenomics tools: kraken and krona. Bug fix for silent tool failures intro...
Bugfixes and unit testing of Trinity and fixes to Broad-specific pipeline scripts
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