v0.5.2

Some assembly stats reporting, some reduction in disk space usage for intermediate bams.

v0.5.1

Push some alignment code out of snakemake and into python scripts (assembly.align_and_fix). Start some more documentation.

v0.5.0

Mosaik builds at Broad now, all hard coded paths removed. Significant increase in documentation. This is now auto-built and hosted http://viral-ngs.readthedocs.org/

v0.4.0

All trinity and VFAT steps wrapped into Python and relevant tool installers made. The entire depletion and assembly pipelines should be portable at this point.

v0.3.4

Bug fix for operating on fat32 file systems.

v0.3.3

Pipelines for ACEGID. There is now a separate and simplified pipeline for reference-guided assembly, specifically made to operate on MiSeq outputs. This is intended for short-term use with the new MiSeqs at run.edu.ng and ucad.sn until the de novo pipeline becomes more portable.

v0.3.2

Tool wrappers have been added for Novoalign and GATK. These do not auto-install; due to licensing reasons, you must have them pre-installed in $PATH / $NOVOALIGN_PATH / $GATK_PATH. With this, the assembly refinement steps have now been fully scripted in assembly.py.

v0.3.1

Happy New Year: some parameter refinements and small fixes.

v0.3.0

latest bugfixes and pipeline tuning for Sierra Leone EBOV analyses

v0.2.4

Refactor how pipes parallelize workload. Current working code for SL EBOV analysis.