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.

Contents

• Getting an account of GSAF's Galaxy instance
• Getting an account on GSAF server-fourierseq
• Getting started with Unix and Perl
• Tips for working with TACC resources
• References (by organism)
• General purpose tools
• Galaxy Workflows
• Microarray data analysis tools
• NGS Data Quality Control Tools
• Mappers / Aligners
• Gene prediction tools
• SNP discovery
• Splice Junction discovery
• Genome Alignment and Visualization
• 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
• Hmmer
• Data compression programs
• Clustering programs - MCL and usearch, uclust
  

Microarray data analysis tools

• MeV
  

NGS Data Quality Control Tools

• Fastx Toolkit
• FastQC
  

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
• 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
  

Splice Junction discovery

• Tophat
  

Genome Alignment and Visualization

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

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)

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

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