Software

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

• Getting an account of GSAF's Galaxy instance NOTE: Galaxy at this site is no longer actively supported.
• Getting an account on GSAF server-fourierseq
• Getting started with Unix and Perl
• Tips for working with TACC resources
• TACC Lonestar workflow scripts
• References (by organism)
• General purpose tools
• Galaxy Workflows
• Microarray data analysis tools
• NGS Data Quality Control Tools
• Mappers / Aligners
• Gene prediction tools
• SNP discovery
• RNA-Seq analysis
• Splice Junction discovery
• Genome Alignment and Visualization
• De novo assembly
• Transcriptome De novo assembly
• 454 Analysis tools
• Useful scripts
• Software users group meetings
• Variant calling
• ZOHO Information
• Extracting barcode split data from SOLiD 5500 XSQ files
• R and R packages

Galaxy Workflows

• RNA-seq workflow
• BWA-SAMTOOLS workflow

General purpose tools

• Blast
• Bioconductor
• Bioperl
• BioMart Perl APIs
• NCBI Eutils
• R
• Python Library
• Graphics programs
• BOOST libraries
• Phred, Phrap, Consed, cross_match, daev
• Picard
• Hmmer
• Data compression programs
• Clustering programs - MCL and usearch, uclust
• ssh - generating keys

Microarray data analysis tools

• MeV

NGS Data Quality Control Tools

• Fastx Toolkit
• FastQC
• Get FASTQ Format

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

• GeneWise
• Geneid
• glimmer3

SNP discovery and Annotation

• Corona-Lite - SOLiD data only
• Breakdancer
• Genome Analysis Tool Kit (GATK)
• MAQ - best for short-read SNP calling; ungapped alignment
• Picard
• SOAP - very versatile: any read length, gapped, paired-end, SNP calling
• SAMTOOLS
• Annovar

RNA-Seq Analysis

• Tophat-Cufflinks-Cuffdiff, ignoring novel transcripts
• Tophat-Cufflinks-Cuffdiff, allowing for novel transcripts
• Removing duplicates from alignment output

Splice Junction discovery

• Tophat- Cufflinks

Genome Alignment and Visualization

• Circos
• IGV
• MaqView
• Mauve
• Affymetrix Integrated Genome Browser: easy to install genome browser. Download here
• SAMStat

De novo assembly

• MIRA
• Velvet
• ABYSS
• Using consed, including editing Mira assemblies
• ABI's SOLiD de novo pipeline
• Phred, Phrap, Consed, cross_match, daev
• Allpaths-LG
• Mosaik - A suite of alignment and reference-guided assembly tools.
• (Newbler, the Roche/454 assembler, is under 454 Analysis tools)

Transcriptome de novo assembly

• Trinity
• SOAPtrans

ABI pipelines

• Small RNA Pipeline

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*

• Sff file manipulation tools - Utilities to convert and manipulate 454 sff files.
• GS De novo assembler - Performs assembly of reads and generates contigs.
• GS Reference mapper - Maps reads to a reference genome and reports consensus and variants.
• GS Amplicon variant analyzer - For detection of variants in amplicon libraries : a small region of interest at very large coverage.
• GS Run processor and run browser - Generally run already by the GSAF, but you might want to re-process image data sometimes.
• Georgiou Lab Amplicon scripts - Matlab scripts...
• BLAST tools - Scripts for quick and dirty blasts of 454 reads and contigs to see what's going on at a global level

Useful scripts

• Convert ABI SOLiD data to fasta fastq
• General parser scripts - scripts for parsing and filtering of fasta, fastq files and output files from different mappers; base space, color space conversion scripts.
• Small rna analysis
• Generation of wig files from mapreads output
• Conversion of mapreads output to GFF, SAM, or BAM format - These utilities can be used to convert mapreads mapping output to base space format
• Generation of gene counts from results of mapping to genome - These scripts can be used to identify the reads that correspond to genes, after mapping to the genome.
• Get Tm (melting temperature), length, and %GC from a bunch of sequences
• Conversion of gene ID's from one form to another (i.e. NCBI to Ensembl & vice-versa)
• Quick tips on GO analysis
• Median polish to consolidate quantitations
• Make a quick venn diagram based on lists in 3 files
• Plot a read length histogram based on sequences in a fasta file
• Reverse complement for fasta files
• Tricks to preprocess SOLiD and 454 data
• Convert BLAST results to GFF

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