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References

Crispr detection softwares

CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007 May 31

CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007 Jun 18;8(1):209 Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P

PILER-CR: Edgar, R.C. (2007)- fast and accurate identification of CRISPR repeats, BMC Bioinformatics, Jan 20;8:18.

Databases

NCBI - Sequence Read Archive (SRA): http://www.ncbi.nlm.nih.gov/sra

NCBI - Genome database: http://www.ncbi.nlm.nih.gov/genome/

Other tools

Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. [PMID: 19451168]

Picard Tools: https://broadinstitute.github.io/picard/

Fastx toolkit: http://hannonlab.cshl.edu/fastx_toolkit/

samtools: https://github.com/samtools/samtools