MAUND

Indel and mutation ratio analysis program for sequencing data.

Installation

#After downloading this repo,
pip install .
#Or install from the github repo, directly
pip install git+https://github.com/ibs-cge/maund.git

Usage

usage: maund.py [-h] [-c COMPARISON_RANGE] [-b WINDOW_BEG] [-e WINDOW_END]
                [-ib IDXSEQ_BEG] [-ie IDXSEQ_END] [-t {A,C,G,T}]
                [-mcut MISMATCH_CUTOFF]
                aseq rgen [files [files ...]]

Run example

maund.py AAAGAAACCCCTCAAGACCTATAAAGTCTATGTTCCAAGATCATCAGAAGTAACCAGCATTATGGACCGGGCTTATGCAGGGAAAATCTACCCCCGAGTCTATCTGGTAATGTACACAGCTGCATAAAAATATTAGTTCTGTTTTTTAGAGCAGGGTTGGCAAACTTTATCCATAAACGAGCATAAAACAAAGAACAGACTGCTGGGTTTGGCCTGCTGGTTGTCACTTGCCAATCCCTGCCTTAGAACAAAGCAATTGCTTTCTCAGCAGATGGTTCATCGTTAAAGAGTTCCAGTTTTTTTAATAACTAAAATCTAATCCTTTTTCACAATGAAAGAAAATAATTTGAAAATTATGTTTTAAGAAATACAAATTAGTCATAATCACATAACTCATGAG tAAaACAAAGaAcAGACTGCTGG 75.fastqjoin 76.fastqjoin
#Run as a module; required for running on Windows:
python -m libmaund AAAGAAACCCCTCAAGACCTATAAAGTCTATGTTCCAAGATCATCAGAAGTAACCAGCATTATGGACCGGGCTTATGCAGGGAAAATCTACCCCCGAGTCTATCTGGTAATGTACACAGCTGCATAAAAATATTAGTTCTGTTTTTTAGAGCAGGGTTGGCAAACTTTATCCATAAACGAGCATAAAACAAAGAACAGACTGCTGGGTTTGGCCTGCTGGTTGTCACTTGCCAATCCCTGCCTTAGAACAAAGCAATTGCTTTCTCAGCAGATGGTTCATCGTTAAAGAGTTCCAGTTTTTTTAATAACTAAAATCTAATCCTTTTTCACAATGAAAGAAAATAATTTGAAAATTATGTTTTAAGAAATACAAATTAGTCATAATCACATAACTCATGAG tAAaACAAAGaAcAGACTGCTGG 75.fastqjoin 76.fastqjoin

Output files

• {input}.{target_seq}.out.Miseq_summary.txt : result summary
• {input}.{target_seq}.out._window.txt : window-read counts
• {input}.{target_seq}.out._aligned.txt: based on alignment of target sequence in a comparison range.