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reStrainingOrder - Mouse Strain Identification

Function A QC tool to identify pure strain or hybrid mouse samples from high-throughput Illumina sequencing experiments that have been aligned to N-masked genomes
Language Perl, HTML, JavaScript
Requirements A functional version of Samtools is required.
Code Maturity Initital Release, seems to work.
Code Released Yes, under GNU GPL v3 or later.
Initial Contact Felix Krueger

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reStrainingOrder is a QC tool for high-throughput mouse sequencing samples that is designed to read in alignment files in SAM/BAM format and determine for reads that cover known SNP positions whether the sample came from a pure mouse strain or whether it is more likely derived from a hybrid cross. For this to work a library must have been aligned to a genome which had all SNP positions masked by the ambiguity base 'N', and aligned using aligners that are capable of using a reference genome which contains ambiguous nucleobases, such as Bowtie 2, HISAT2, STAR, or Bismark.

It is probably worth mentioning that the determination of overlaps correctly handles the CIGAR operations M (match), D (deletion in the read), I (insertion in the read) and N (skipped regions, used for splice mapping by HISAT2, STAR, or TopHat). Other CIGAR operations are currently not supported.

reStrainingOrder is available on Github where you can find the latest development version reStrainingOrder (Github)

Here you can access the documentation for more information on the reStrainingOrder workflow reStrainingOrder User Guide (Markdown)

Here is an example reStrainingOrder report for a pure strain sample (Bisulfite-seq sample SRR6994034) Pure Strain report

Here is an example reStrainingOrder report for a hybrid 129S1/CAST_EiJ sample (Bisulfite-seq sample SRR377634) 129S1/CAST Hybrid report