HybPiper 1.2: Target Finesse, Unpaired Reads, and Python 3

Features

• Added --unpaired flag. When using paired-end sequencing reads, a third read file may be specified with this flag. Reads will be mapped to targets separately, but will be used along with paired reads in contig assembly.

• Added --target flag. Adds the ability to choose which of the reference sequences is used for each gene. If --target is a file (tab-delimited file with one gene and one target name per line), HybPiper will use that. Otherwise --target can be the name of one reference. HybPiper will only use targets with the specified name in the Alignment/Exon Extraction phase. All other targets for that locus will only be used in the Mapping/Read Sorting phase.

• Added --timeout flag, which uses GNU Parallel to kill processes (i.e. Spades or Exonerate) if they take X percent longer than average. Use if there are a lot of stuck jobs (--timeout 1000)

• Python 3 compatibility

Bug Fixes

• Can accommodate Solexa FASTQ paired headers
• Fixed spades_runner.py not recognizing --cpu on redos
• Prints more meaningful messages for some common errors
• Can accommodate prefix not being in current directory
• Deletes sorted reads on restart to prevent double counting reads.
• spades_runner.py will now respect --kvals
• Added initial call to log for reads_first.py