Tools   Select Another Resource Report Type

https://code.google.com/p/breseq/

A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data intended for haploid microbial genomes.

Proper citation: breseq (RRID:SCR_010810) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/cga/mutsig

Software that analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes.

Proper citation: MutSig (RRID:SCR_010779) Copy   

•   Source: SciCrunch Registry

http://svdetect.sourceforge.net/Site/Home.html

Software application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identify structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. It is compatible with SOLiD and Illumina (>=1.3) reads.

Proper citation: SVDetect (RRID:SCR_010812) Copy   

•   Source: SciCrunch Registry

http://snps.biofold.org/phd-snp/phd-snp.html

It is based a SVM-based classifier.

Proper citation: PhD-SNP (RRID:SCR_010782) Copy   

•   Source: SciCrunch Registry

http://mmb.pcb.ub.es/PMut/

A software aimed at the annotation and prediction of pathological mutations.

Proper citation: PMut (RRID:SCR_010783) Copy   

•   Source: SciCrunch Registry

http://www.integralife.com/

Commercial tissue bank for human tissues.

Proper citation: Integra Life Sciences (RRID:SCR_010741) Copy   

•   Source: SciCrunch Registry

https://www.broadinstitute.org/scientific-community/science/programs/genome-sequencing-and-analysis/computational-rd/computational-

Software tool as whole genome shotgun assembler that can generate high quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers.

Proper citation: ALLPATHS-LG (RRID:SCR_010742) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Main_Page

A de novo whole-genome shotgun (WGS) DNA sequence assembler.

Proper citation: Celera assembler (RRID:SCR_010750) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/soapdenovo.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 24,2023. Software tool for de novo assembly of human genomes with massively parallel short read sequencing.Short-read assembly method that can build de novo draft assembly for human sized genomes.Software package for assembling short oligonucleotide into contigs and scaffolds.

Proper citation: SOAPdenovo (RRID:SCR_010752) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.nyu.edu/wordpress/projects/sutta/

A new De Novo DNA sequence assembler based on global search-methods in order to contain the complexity of the assembly problem.

Proper citation: SUTTA (RRID:SCR_010754) Copy   

•   Source: SciCrunch Registry

https://www.hgsc.bcm.edu/content/atlas2

A next-generation sequencing suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in WECS data.

Proper citation: Atlas2 (RRID:SCR_010756) Copy   

•   Source: SciCrunch Registry

http://odin.mdacc.tmc.edu/~wwang7/FamSeqIndex.html

A computational tool for calculating probability of variants in family-based sequencing data.

Proper citation: FamSeq (RRID:SCR_010760) Copy   

•   Source: SciCrunch Registry

http://www.moleculardevices.com/Products/Software/GenePix-Pro.html

Industry standard microarray image analysis software because of its unique combination of imaging and analysis tools, visualizations, automation capabilities, performance and intuitive workflows.

Proper citation: GenePix Pro (RRID:SCR_010969) Copy   

•   Source: SciCrunch Registry

http://berry.engin.umich.edu/oligoarray2_1/

A free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction.

Proper citation: OligoArray (RRID:SCR_010961) Copy   

•   Source: SciCrunch Registry

http://www.complex.iastate.edu/download/Picky/

A software tool for selecting optimal oligonucleotides (oligos) that allows the rapid and efficient determination of gene-specific oligos based on given gene sets, and can be used for large, complex genomes such as human, mouse, or maize.

Proper citation: Picky (RRID:SCR_010963) Copy   

•   Source: SciCrunch Registry

http://pbil.univ-lyon1.fr/roso/help.php

A software to design optimized oligonucleotide probes (size over 25 nucleotides) for microarrays.

Proper citation: ROSO (RRID:SCR_010967) Copy   

•   Source: SciCrunch Registry

http://www.cbrc.kaust.edu.sa/hmcan/

A Hidden Markov Model based software tool that is developed to detect histone modification in cancer ChIP-seq data.

Proper citation: HMCan (RRID:SCR_010858) Copy   

•   Source: SciCrunch Registry

http://www.cos.uni-heidelberg.de/index.php/n.ha

Software for detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets.

Proper citation: COPS (RRID:SCR_010852) Copy   

•   Source: SciCrunch Registry

http://www.illumina.com/software/genomestudio_software.ilmn

Visualize and analyze data generated by all of Illumina''s platforms.

Proper citation: GenomeStudio (RRID:SCR_010973) Copy   

•   Source: SciCrunch Registry

http://www.bu.edu/jlab/wp-assets/ComBat/Abstract.html

Adjusting batch effects in microarray expression data using Empirical Bayes methods.

Proper citation: ComBat (RRID:SCR_010974) Copy   

•   Source: SciCrunch Registry