broadinstitute/viral-ngs: v1.14.0

A set of scripts and tools for the analysis of viral NGS data. More detailed documentation can be found at http://viral-ngs.readthedocs.org/ This includes installation instructions, usage instructions for the command line tools, and usage of the pipeline infrastructure. v1.14.0 Release Notes New: read_utils.align_and_fix() now has an option--skipMarkDupes since samtools depth can segfault if if duplicate reads are marked reports.align_and_plot_coverage() can now use Novoalign as the aligner rather the default BWA mem Fixed: align_rna memory raised to 36 GB in Snakemake pipeline metagenomics.coverage_lca() is now hardened to missing taxids Changed/Updated: For align_rna, "sensitive" option is now disabled by default for BWA mem pytest 2.9.1 -> 3.0.