Exome 解析に使うツール群のリンク
- FastQC
http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
- FASTX-Toolkit
http://hannonlab.cshl.edu/fastx_toolkit/
- Burrows-Wheeler Aligner
http://bio-bwa.sourceforge.net/
https://github.com/lh3/bwa
git clone https://github.com/lh3/bwa.git
- SAMtools
http://samtools.sourceforge.net/
svn co https://samtools.svn.sourceforge.net/svnroot/samtools/trunk/samtools
- Picard
http://picard.sourceforge.net/
svn co https://picard.svn.sourceforge.net/svnroot/picard/trunk picard
- bedtools - bedtools: a flexible suite of utilities for comparing genomic features.
http://code.google.com/p/bedtools/
https://github.com/arq5x/bedtools
git clone https://github.com/arq5x/bedtools.git
- ANNOVAR website
http://www.openbioinformatics.org/annovar/
作者にメールする必要がある
- GATK
http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit
git clone https://github.com/broadgsa/gatk.git
- Dindel: Accurate indel calls from short-read data - Wellcome Trust Sanger Institute
http://www.sanger.ac.uk/resources/software/dindel/
wget -r -np -nd ftp://ftp.sanger.ac.uk/pub4/resources/software/dindel -P dindel
TruSeq Exome 関連
- ターゲットリシーケンスのためのカバレッジの最適化 http://www.illuminakk.co.jp/pdf/TN_Targeted_Resequencing.pdf
- Optimizing Coverage for Targeted Resequencing http://www.illumina.com/documents/products/technotes/technote_optimizing_coverage_for_targeted_resequencing.pdf
- TruSeq_exome_targeted_regions.hg19.chr.bed.gz => iCom だと表記が次のように異なっている TruSeq-Exome-Targeted-Regions-BED-file.gz
- TruSeqExome1.1_installer.tgz => iCom だと表記が次のように異なっている TruSeq Exome Run Quality scripts