SeqCapAnalyst, a pipeline for analyzing Sequence Capture data in avian malaria
SeqCapAnalyst is a pipeline to process .fastq files, producing the standard files as well as statistics useful for singling out good targets for Sequence Capture probes. Rather than speed, it is optimized for flexibility and ease of modification. SeqCapAnalyst is predominantly written in bash, with one module written in Python. The pipeline was tested on sequence capture data which was obtained f