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