Version 2.2

Major changes include:

• Adds an option for a pipeline that keeps a smaller, less comprehensive set of output files
• kmerFind.py: locates reads with a specific barcode, allowing for mismatches. Barcoded reads can either be trimmed or masked with N
• BARCODE: is the pipeline module wraper for kmerFind.py
• TRIM: added poly-base trimming, allowing for removal of long strings of
  the same base from either end of the read and parallelized trimming
• BLASTQC: allow for short reads (shorter than 50bp)
• launcher.sh: allow for running pre-configured pipeline instances in parallel using a csv config file
• run_bcl2fastq.sh: run Illumina bcl2fastq v2.17

Version 2.1

• Renamed various internal and output files
• BLAST: don’t resample reads if blast already run. numerous tweaks.
• BOWTIE: allow for single end
• PIPELINE: added more parameters to simplify run types. bug fixes.
• POST: allow setting of GUID
• STAR: update for STAR 2.4.0 or later. tweaks and bug fixes.
• HTSEQ: exon and intron counting by intersection-strict
• STATS: added simple (i.e. quiet) mode for output.
• TRIM: allow for parallelized trimming.
• VERSE: added Verse module.
• ngs.sh: bug fixes, minor tweaks.
• parseBlast.py: included more target species, bug fixes.
• trimReads.py: allow for parallelized trimming.
• combineGeneCounts.py: added to merge gene count files based on intersection or union operators.

Version 2.0

This is a major release version. Some of the notable changes are included below. See individual module files for more information.

• Updated STAR parameters. The new STAR parameters are set such that only one read in a read pair needs to map. See the STAR module for additional parameter changes. Because STAR parameters have been changed the STAR module in version 2 will produce different alignments than version 1.
• Update HTSEQ parameters. The HTSeq counting type has been changed for exons and the ability to count introns and mitochondria has been added. Because HTSEQ parameters have been changed the HTSEQ module in version 2 will produce different read counts than version 1.
• More version information is generated for all commands used and simplified command logging allowing for better data provenance.
• Improved FASTQC and BLASTQC output.

Initial release

This is the initial pipeline release.