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A pipeline for mapping insertion mutants from whole genome shotgun data

Project description

This package provides software for identifying the genome insertion points random mutants generated by insertional mutagenesis, which have been sequenced as a pool.

The package will install two executables: aimhii and extract_chimeras.

aimhii will run a full analysis starting from sequence data (a FASTQ file), genome sequence, and insert sequence. extract_chimeras just runs the last step of this analysis, assuming you already have a BAM file and a concatenated genome-insert sequence.

For details see the project website https://github.com/granek/aimhii/

Changes in v0.5.5: Added filter_bam.filter_chimeric_reads to pipeline extract only putative junction reads from BWA output. Shifted to hosting on github.

Changes in v0.5.4: Added –plot option to aimhii and shifted a few remaining “prints” to logging

Changes in v0.5.3: Shifted debugging prints to logging and added scripts for generating synthetic sequences

Changes in v0.5.2: Lowered pysam version requirement to allow installation using apt-get in Debian v8.

Changes in v0.5.1: Fixed problem with missing DESCRIPTION.rst.

Project details


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