This contains a simple sequence counter intended to count the occurences of a set of predefined sequences in a fastq file.
This contains a simple sequence counter intended to count the occurences of a set of predefined sequences in a fastq file. First, all occuring read sequences are counted. Then, these counts are mapped to a set of predefined sequences.
It also contains a wrapper for NGmerge to merge overlapping paired-end sequenced reads.
Reads and sequences can also be trimmed to exclude flanking regions that are not of interest, e.g. adapters and primers.
This project is intended for use with pypiegraph2 and mbf packages available on pypi and github for job generation and scheduling.