Software

The following is a categorized list of software available through the GSAF. Each page lists a summary of the software, the hardware it is currently installed on, links to user documentation, and helpful tips.

Contents

Galaxy Workflows

General purpose tools

Microarray data analysis tools

MeV

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

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

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

Space shortcuts

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Software