v1.1.3

Illumina demux related bug fixes and dependency cleanups.

v1.1.2

Fixes in Mosiak wrapper, easy deploy mechanism, and lint-inspired code cleanups.

v1.1.1

Improvements to Illumina demultiplexing and miseq fastq to bam conversions.

v1.1.0

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.

v1.0.0

Tweaks to pipeline defaults. Prep for manuscript.

v0.9.1

NCBI submission tools, MAFFT multi-aligner, misc bug fixes

v0.9.0

Intrahost variant calling, similar to as described in Gire et al, but with tolerance for consensus level indels and hooks for future improvements.

v0.5.5

Reduce blastn (depletion) memory footprint for large data sets, begin some ground work on intrahost variant calling.

v0.5.4

Bug fixes with Mosaik wrapper and Novoalign wrapper (BAM headers). Improvements to Travis-CI framework.

v0.5.3

Increased JVM memory to Butterfly (Trinity) and improved / fixed / cleaned up a number of report generation steps.