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Tufts Medical School Bioinformatic cluster installed software tools
under construction
A local software repository is available to meet the dynamic needs of individual Medical researchers. This effort is maintained by Dr. Lax Iyer(lax.iyer@tufts.edu). A directory of available commandline tools can be found at , Joshua Ainsley(Joshua.Ainsley@tufts.edu), and Gavin Schnitzler(GSchnitzler@tuftsmedicalcenter.org). Please contact them to address specific software needs or requests.
Packages for Next Generation Sequencing analysis have been set up in filesystem /cluster/tufts/ngsp/ngsp/bin/
Programs in this directory can be accessed using the module command,
> module add ngs
which adds the path /cluster/tufts/ngsp/ngsp/bin to a user's PATH.
Available software:
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end) Bowtie
TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie. TopHat runs on Linux and OS X. cufflinks TopHat
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols. Cufflinks
SAMtools: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format SAMtools
BamTools provides both a programmer's API and end-user's toolkit for handling BAM files BamTools
Mothur:This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community Mothur
RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The new RSEM package (rsem-1.x) provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. It can also generate genomic-coordinate BAM files and UCSC wiggle files for visualization. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels RESM