Fixed: two issues corrected in using bwa mem for alignment (see commit) Changed: a few internal function calls (see commits
New: Improvements to the pipeline to support single-end reads in additional stages, including the d...
This release fixes a consistent major failure mode (which only emerged recently) when executing most...
Assembly improvements including gap2seq and an alternative assembler (SPAdes). This will be replaced...
A set of scripts and tools for the analysis of viral NGS data. More detailed documentation can be f...
Fixed: CheckIlluminaDirectory now creates symlinks only if necessary Fix plot_coverage for cases wh...
What's Changed increase tsv_join default mem 7->15 GB by @tomkinsc in #406 update pangolin containe...
Fixed: fix position output for genome features falling oob during annotation in snakemake pipeline:...
Fixed: Fix issues related to Trinity on certain environments (#900) allow for flexibility in gatk v...
New: assembly.order_and_orient() now supports --outAlternateContigs to output sequences (in FASTA...
New: New BWA-based LCA metagenomics function: metagenomics. align_rna() Align to metagenomics bwa i...
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: scaffolder uses ambiguous alignments when no unambiguous ones exist (#904) add function to ass...
Changed: Demultiplexing from Illumina basecalls is now more permissive of varying input directory [...
Changed: improve handling of possible feature table IDs [#846] Fixed: genome feature annotation t...
New: Improvements to the pipeline to support single-end reads in additional stages, including the d...
This release fixes a consistent major failure mode (which only emerged recently) when executing most...
Assembly improvements including gap2seq and an alternative assembler (SPAdes). This will be replaced...
A set of scripts and tools for the analysis of viral NGS data. More detailed documentation can be f...
Fixed: CheckIlluminaDirectory now creates symlinks only if necessary Fix plot_coverage for cases wh...
What's Changed increase tsv_join default mem 7->15 GB by @tomkinsc in #406 update pangolin containe...
Fixed: fix position output for genome features falling oob during annotation in snakemake pipeline:...
Fixed: Fix issues related to Trinity on certain environments (#900) allow for flexibility in gatk v...
New: assembly.order_and_orient() now supports --outAlternateContigs to output sequences (in FASTA...
New: New BWA-based LCA metagenomics function: metagenomics. align_rna() Align to metagenomics bwa i...
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: scaffolder uses ambiguous alignments when no unambiguous ones exist (#904) add function to ass...
Changed: Demultiplexing from Illumina basecalls is now more permissive of varying input directory [...
Changed: improve handling of possible feature table IDs [#846] Fixed: genome feature annotation t...
New: Improvements to the pipeline to support single-end reads in additional stages, including the d...
This release fixes a consistent major failure mode (which only emerged recently) when executing most...
Assembly improvements including gap2seq and an alternative assembler (SPAdes). This will be replaced...
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