SNP Array Software |
| Name |
Description |
Path on server |
Version |
| PennCNV |
Copy Number Variation (CNV) detection from signal intensity data from Illumina and Affymetrix arrays (http://www.openbioinformatics.org/penncnv/) |
/software/cnvpipeline/penncnv/ |
2010May01 |
| QuantiSNP |
Copy Number Variation (CNV) detection from signal intensity data from Illumina arrays (http://www.well.ox.ac.uk/QuantiSNP/) |
/software/cnvpipeline/QuantiSNP/quantisnp/
|
2.3 Beta |
| CNV Pipeline |
Simplify all stages of predicting and analyzing CNVs, from running prediction algorithms and combining their results to visualizing the raw data and designing qPCR primers for confirmation (http://www.yale.edu/state/Homepage.htm) |
/software/cnvpipeline |
1.0 |
| Eigenstrat |
Detects and corrects for population stratification in genome-wide association studies (http://genepath.med.harvard.edu/~reich/Software.htm) |
/software/eigenstrat |
3.0 |
| GenePool |
Provides analysis tools for the detection of shifts in relative allele frequency between pooled genomic DNA from cases and controls using SNP-based genotyping microarrays (http://genepool.tgen.org/) |
/software/GenePool |
0.8.2 |
| IMPUTE2 |
Estimating ("imputing") unobserved genotypes in SNP association studies (https://mathgen.stats.ox.ac.uk/impute/impute_v2.html) |
/software/impute |
2 |
Sequencing Software |
| Name |
Description |
Path on server |
Version |
| Fastx Toolkit |
Preprocess the FASTA/FASTQ files before mapping the sequences to the genome (http://hannonlab.cshl.edu/fastx_toolkit/) |
Accessible from any folder |
0.0.13 |
| Fastqc |
Quality control tool for high throughput sequence data (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) |
/software/sequencing/FastQC |
0.9 |
| bwa |
Burrows-Wheeler Alignment Tool (http://bio-bwa.sourceforge.net/bwa.shtml) |
/software/sequencing/bwa_latest |
0.5.9 |
| Picard tools |
Utilities that manipulate SAM files and SAM-JDK creating new programs that read and write SAM files. (http://picard.sourceforge.net/) |
/software/sequencing/picard_latest |
1.47 |
| 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. (http://samtools.sourceforge.net/) |
/software/sequencing/samtools_latest |
0.1.16 |
| GATK |
Coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner (http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit ) |
/software/sequencing/GATK_latest |
1.0.5777 |
| Dindel |
A program for calling small indels from short-read sequence data. It is currently designed to handle only Illumina data. (http://www.sanger.ac.uk/resources/software/dindel/ ) |
/software/sequencing/dindel_latest |
1.01 |
| BEDtools |
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. (http://code.google.com/p/bedtools/) | /software/sequencing/BEDTools_latest |
2.12 |
| PINDEL |
Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. (https://trac.nbic.nl/pindel/wiki/UserManual) | /software/sequencing/Pindel_latest |
0.2 |
Data |
| Name |
Description |
Path on server |
Last update |
| HapMap LD data |
LD data of 11 populations in HapMap phase 3 |
/data/HapMap/LD |
2009-4-20 |
| 1000 Genome genotype |
Genotype data of 1000 genome project (African, Asian, European) |
/data/1000G/genotype |
2011-3-11 |