Generic collection of python Utilities and Wrapper for DNA/NGS data manipulation for python 2.7
For now it includes BWA, Blast and Smith–Waterman wrappers as well as higher level functionality:
- FastqFT : Filter fastq file based on quality and adapter trimming
- RefMasker : Align a fasta reference against several fastq queries and mask homologies in the reference file
- pySamTools : Manipulate aligned reads manipulation though pysam
- Utilities : Library of simple generic functions to manipulate paths and file, interact with command line interpreter and so on