CREST 结构变异检测工具安装指南
CREST (Clipping Reveals Structure) is a new algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data.
article:CREST maps somatic structural variation in cancer genomes with base-pair resolution (2011)
tar zxvf CREST.tgz
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Requirements:
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Before running CREST, you need to make sure that several pieces of software
and/or modules are installed on the system:
1. BLAT software suite, especially blat, gfClient, and gfServer. BLAT
can be obtained from these links:
BLAT for academic use: http://www.soe.ucsc.edu/~kent
BLAT commercial license: http://www.kentinformatics.com/
2. CAP3 assembly program, available here:
CAP3 for academic use: http://seq.cs.iastate.edu/cap3.html
CAP3 commercial license: Contact Robin Kolehmainen at Michigan Tech,
rakolehm@mtu.edu or (906)487-2228.
3: SAMtools library for accessing SAM/BAM files, available from SourceForge:
SAMtools: http://sourceforge.net/projects/samtools/files/
4. BioPerl and Bio::DB::Sam modules. They are usually available as
packages on most Linux distributions, but are also available at this link:
BioPerl: http://www.bioperl.org/
Bio::DB::Sam: http://search.cpan.org/~lds/Bio-SamTools/lib/Bio/DB/Sam.pm
Important: you must install SAMtools library before install Bio::DB::Sam.
5. ptrfinder is needed if you want to remove short tandem repeat mediated
SVs, the executable is included in the download package, put it on the path.
use conda:
conda install -c bioconda perl-bio-db-sam
conda install -c bioconda perl-bioperl
BLAT software suite ：
$echo $MACHTYPE
$x86_64-redhat-linux-gnu
$MACHTYPE=x86_
hard write $target_genome $dir_2bit $blat_server $blat_port in CREST.pl should be changed.
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