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Software

The following is a categorized list of software available through the UT GSAF and/or TACC's life sciences group. Each page lists a summary of the software, the hardware it is currently installed on, links to user documentation, and helpful tips.

Many of these are available via the TACC module system (use module keyword or module spider to search).

The current listing of modules and versions available on Lonestar is also posted here.

In addition, the BioITeam maintains executables in /corral-repl/utexas/BioITeam/bin; we advise adding this directory to your path.

Contents

Galaxy Workflows

General purpose tools

Microarray data analysis tools

NGS Data Quality Control Tools

Mappers/Aligners

  • mapreads SOLiD data only, ungapped alignment
  • MAQ - best for short-read SNP calling; ungapped alignment
  • muscle - "old school" aligner - good for 454 amplicons
  • SOAP - very fast and versatile: any read length, gapped, paired-end, SNP calling
  • SSAHA & SSAHA2 - like Maq, fast for ungapped mapping - SNP calling, contig placement to reference, etc.
  • Bowtie - very fast, ungapped alignment. Does not support color space data
  • SHRiMP - A sensitive and accurate mapper. Supports color space data and gapped alignment.
  • BFAST - BLAT-like short read mapper. Natively supports SOLiD colorspace short reads.
  • BWA - The successor to MAQ; a BW mapper, but which allows for gaps and handles colorspace natively.
  • GMAP and GSNAP - Mappers for cDNA and very sensitive detection of short indels.
  • Mosaik - A suite of alignment and reference-guided assembly tools.
  • See Category:Mapper for more details.

Gene prediction tools

SNP discovery and Annotation

RNA-Seq Analysis

Splice Junction discovery


Genome Alignment and Visualization


De novo assembly

Transcriptome de novo assembly

ABI pipelines

454 Analysis tools
Current Roche/454 software versions on Fourierseq are all 2.5.3. Tarballs of various 454 software versions are available at /home/daras/454sw*


Useful scripts


Software users group meetings

  • Small-rna data analysis - Lessons learned during Sullivan data analysis
  • Mapping of short reads - Comparison of few publicly available mapping tools
  • No labels
Page: ABI's SOLiD de novo pipeline Page: ABYSS Page: Annovar Page: BFAST Page: Bioconductor Page: BioMart Perl APIs Page: Blast Page: BLAST tools Page: BOOST libraries Page: Bowtie Page: Breakdancer Page: BWA Page: BWA-SAMTOOLS workflow Page: CASAVA Page: Circos Page: CGView Page: Clustering programs - MCL and usearch, uclust Page: Conversion of gene ID's from one form to another (i.e. NCBI to Ensembl & vice-versa) Page: Conversion of mapreads output to GFF, SAM, or BAM format Page: Convert ABI SOLiD data to fasta fastq Page: Cufflinks Page: Data compression programs Page: Extracting barcode split data from SOLiD 5500 XSQ files Page: FastQC Page: Fastx Toolkit Page: Galaxy Setup Page: Geneid Page: General parser scripts Page: Generation of gene counts from results of mapping to genome Page: Generation of wig files from mapreads output Page: GeneWise Page: Genome Analysis Tool Kit Page: Getting an account on GSAF server-fourierseq Page: Get Tm (melting temperature), length, and %GC from a bunch of sequences Page: glimmer3 Page: GMAP and GSNAP Page: Graphic programs Page: GS Amplicon variant analyzer Page: GS De novo assembler Page: GS Reference mapper Page: GS Run processor and run browser Page: Hmmer Page: IGV Page: Make a quick venn diagram based on lists in 3 files Page: mapreads Page: MAQ Page: MaqView Page: Median polish to consolidate quantitations Page: MegaMapper Page: MeV Page: MIRA Page: Mosaik Page: muscle Page: Phred, Phrap, Consed, cross_match, daev Page: Picard Page: Plot a read length histogram based on sequences in a fasta file Page: Python Library Page: Quick tips on GO analysis Page: R and R packages Page: Reverse complement for fasta files Page: RNA-seq workflow Page: SAMTOOLS Page: Sff file manipulation tools Page: SHRiMP Page: Small rna analysis Page: Small-rna data analysis Page: Small RNA Pipeline Page: SOAP Page: SOAPtrans Page: Tips for working with TACC resources Page: Tophat- Cufflinks Page: Tophat-Cufflinks-Cuffdiff, allowing for novel transcripts Page: Tophat-Cufflinks-Cuffdiff, ignoring novel transcripts Page: Tricks to preprocess SOLiD and 454 data Page: Trinity Page: Variant calling Page: Velvet Page: ZOHO Information Page: Removing duplicates from alignment output Page: SAMStat Page: TACC Lonestar workflow scripts Page: Get FASTQ Format Page: launcher_creator.py Page: Wrappers For TACC Page: ssh - generating keys