NCURSE -programming library for text-based user interfaces
http://codybonney.com/installing-the-ncurses-library-in-centos-6-5/
sudo yum install ncurses-devel
Cutadapt - adapter sequence trimming
http://cutadapt.readthedocs.org/en/latest/index.html
Trimmomatic: A flexible read trimming tool for Illumina NGS data
http://www.usadellab.org/cms/?page=trimmomatic
FastQC - quality check of fastq file
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Bowtie - short read aligner
http://bowtie-bio.sourceforge.net/index.shtml
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Tophat - splice junction mapper for RNA-Seq reads (need Bowtie)
https://ccb.jhu.edu/software/tophat/index.shtml
samtools - tools for manipulating alignments in the SAM(Sequence Alignment/Map) format,
http://samtools.sourceforge.net/
picard - tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF
http://broadinstitute.github.io/picard/
HTSeq - Python package that provides infrastructure to process data from high-throughput sequencing assays
http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html
MACS - Model-based Analysis for ChIP-Seq
http://liulab.dfci.harvard.edu/MACS/
PeakSplitter - Subdivision of ChIP-seq/ChIP-chip regions into discrete signal peaks
http://www.ebi.ac.uk/research/bertone/software
R - free software environment for statistical computing and graphics
https://www.r-project.org/
IGV - Integrative Genomics Viewer
https://www.broadinstitute.org/igv/
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