Move software dependencies to bioconda for greater reliability / cross-platform compatibility. Code fixes and stylistic cleanups. Migrate snakemake config file from JSON to YAML to allow for in-line documentation and comments. Initial work on metagenomic tools. Improvements to easy deploy
New: [Nothing] Fixed: the conda channel order has been corrected to reflect the bioconda-preferre...
Tune nucmer parameters in scaffolding step to tolerate more diverse viruses (HIV, Influenza). Misc b...
New: Dockerfile for viral-ngs now available to build containerized installs (likely moving to vir...
Bug fixes, tested support for multi-segment genomes, and ability to download FASTAs, feature tables,...
New: New BWA-based LCA metagenomics function: metagenomics. align_rna() Align to metagenomics bwa i...
New: The Snakemake pipeline can now source database files from S3, GS, or SFTP if given protocol-pr...
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...
Small fixes OSX compatibility fixes (most steps should work, with the exception of intrahost and m...
New: Improvements to the pipeline to support single-end reads in additional stages, including the d...
Quick fixes: Revert fasta indexing to samtools instead of pysam (for py3 threaded stability). Fix ...
Fixes: easy deploy script has been updated in a few more places to reflect shift to conda-based en...
Implementation of basic metagenomics tools: kraken and krona. Bug fix for silent tool failures intro...
New: assembly.order_and_orient() now supports --outAlternateContigs to output sequences (in FASTA...
Changed: Demultiplexing from Illumina basecalls is now more permissive of varying input directory [...
New: [Nothing] Fixed: the conda channel order has been corrected to reflect the bioconda-preferre...
Tune nucmer parameters in scaffolding step to tolerate more diverse viruses (HIV, Influenza). Misc b...
New: Dockerfile for viral-ngs now available to build containerized installs (likely moving to vir...
Bug fixes, tested support for multi-segment genomes, and ability to download FASTAs, feature tables,...
New: New BWA-based LCA metagenomics function: metagenomics. align_rna() Align to metagenomics bwa i...
New: The Snakemake pipeline can now source database files from S3, GS, or SFTP if given protocol-pr...
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...
Small fixes OSX compatibility fixes (most steps should work, with the exception of intrahost and m...
New: Improvements to the pipeline to support single-end reads in additional stages, including the d...
Quick fixes: Revert fasta indexing to samtools instead of pysam (for py3 threaded stability). Fix ...
Fixes: easy deploy script has been updated in a few more places to reflect shift to conda-based en...
Implementation of basic metagenomics tools: kraken and krona. Bug fix for silent tool failures intro...
New: assembly.order_and_orient() now supports --outAlternateContigs to output sequences (in FASTA...
Changed: Demultiplexing from Illumina basecalls is now more permissive of varying input directory [...
New: [Nothing] Fixed: the conda channel order has been corrected to reflect the bioconda-preferre...
Tune nucmer parameters in scaffolding step to tolerate more diverse viruses (HIV, Influenza). Misc b...
New: Dockerfile for viral-ngs now available to build containerized installs (likely moving to vir...
DOI
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