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A collection of free-to-use scripts

License: GNU General Public License v2.0

Python 100.00%

bslaby-scripts's Introduction

scripts

A collection of free-to-use scripts

avgcov_from_samtoolsout.py

This script takes the output of samtools depth of a mapping of reads to an assembly and calculates the mean coverage for each contig. samtoolsout is the output of samtools depth the output is written to standard output

mkBinFasta.py

This script takes the comma-separated output table of a binning tool ["contigname,binname", e.g. concoct (https://github.com/BinPro/CONCOCT, http://www.nature.com/nmeth/journal/v11/n11/full/nmeth.3103.html)] and and the binned assembly fasta and creates a fasta file and a list of contigs for each bin. clusterfile is the comma-separated binning output table contigfasta is the assembly fasta that was used for binning

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