analyzing indels generated by CRISPR or other nucleases via deep sequencing

companion to paper detailing the generation of stable germ-line mutants in the mosquito Aedes aegypti

ben matthews 12/26/2014
Ben.Matthews@rockefeller.edu
github repository
The companion pre-print can be found on bioRxiv:
Genome-engineering with CRISPR-Cas9 in the mosquito Aedes aegypti

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Contained in this repository (as of Jan. 22, 2015): analysis notebooks associated with our bioRxiv pre-print
In progress: generic code for analysis of a single sequencing library

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I use Anaconda as a python distribution on both MacOS and RHEL Linux.

software requirements and tested versions:

1. gmap/gsnap [http://research-pub.gene.com/gmap/] version 10-09-2014
   
2. pysam [https://github.com/pysam-developers/pysam] version 0.8.0
   
3. samtools/htslib [http://www.htslib.org] version 1.1
   

python package requirements:

1. pysamstats [https://github.com/alimanfoo/pysamstats] version 0.16
   
2. seaborn [http://web.stanford.edu/~mwaskom/software/seaborn/] version 0.4.0
   

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output:

1. sorted .bam files for each sample
   
2. .variant.stats file summarizing indel/SNP rates for each sample
   
3. figure output for panels in Figures 2-4
   

input:

1. directory of .fastq files with numbered samples denoted by SX.fastq (the default output from an Illumina MiSeq instrument)
   
2. fasta file to serve as a 'genome' for the gapped alignments