##What it does:
Extracts genes using a consensus sequence.
##How it works:
- Creates local short read databases from fastq file for blast.
- Blasts reference fastas against the short read blast databases.
- Collects blast hits into .hits files.
- Creates new small fastq files from .hits files.
- Uses bwa to create gene alignments.
- Uses bcftools, samtools, and novocraft to create consensus sequences.
##Note
This is still very much a work in progress. The cgap file needs to be split into multiple functions instead of the monolithic class in which it currently resides.
##Docker
All the programs for this pipeline are compiled in a docker image on the docker hub.
docker run -itv <directory>:/work theculliganman/cgap /bin/bash