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http://www.scienceexchange.com/facilities/zyagen

A commercial service organization from Zyagen.

Proper citation: Zyagen (RRID:SCR_005295) Copy   

•   Source: SciCrunch Registry

https://github.com/songlab/chance

A standalone software package for ChIP-seq quality control and protocol optimization.

Proper citation: CHANCE (RRID:SCR_005330) Copy   

•   Source: SciCrunch Registry

http://users-birc.au.dk/biopv/php/fabox/

Tools for splitting, joining and otherwise manipulating FASTA format sequence files. The first tools in the toolbox is for manipulating fasta headers, cropping alignments and doing some sequence comparison allowing users to combine the description of data (often in excel spreadsheets) with the actual data (often DNA sequences). Also, producing correct input files for a range of programs seems to be problematic for the average user. Hence, some converters in some of the services have been included as well as some stand-alone converters. The converters are not necessarily meant to provide the final input file, but you''ll get a valid input file for Arlequin, MrBayes etc. - that you may further edit so it suit your needs. This means that you may need to combine several of the tools to finish your handling - but it keeps it relatively simple to use. Please note that FaBox is written in PHP and ONLY RUNS ON A WEBSERVER.

Proper citation: FaBox (RRID:SCR_005350) Copy   

•   Source: SciCrunch Registry

http://info.gersteinlab.org/PeakSeq

A software program for identifying and ranking peak regions in ChIP-Seq experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from a control experiment and outputs a file with peak regions ranked with increasing Q-values.

Proper citation: PeakSeq (RRID:SCR_005349) Copy   

•   Source: SciCrunch Registry

http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/AnneOTate.cgi

A web based search tool to help you gain an overview of the set of articles (up to 25,000 most recent articles) retrieved by a PubMed query. Once you enter a query, you can select different types of summary information to view: Important words, Topics, Authors, Affiliations, Journals, Year, Clustered by topic.

Proper citation: Anne O'Tate (RRID:SCR_005340) Copy   

•   Source: SciCrunch Registry

http://cgs.csail.mit.edu/gem/

Java software for studying protein-DNA interaction using ChIP-seq / ChIP-exo data. It links binding event discovery and motif discovery with positional priors in the context of a generative probabilistic model of ChIP data and genome sequence, resolves ChIP data into explanatory motifs and binding events at unsurpassed spatial resolution. GEM reciprocally improves motif discovery using binding event locations, and binding event predictions using discovered motifs.

Proper citation: GEM (RRID:SCR_005339) Copy   

•   Source: SciCrunch Registry

http://mirnylab.bitbucket.org/hiclib/index.html

An Software resource

Proper citation: Hiclib (RRID:SCR_005535) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.toronto.edu/shrimp/

A software package for aligning genomic reads against a target genome.

Proper citation: SHRiMP (RRID:SCR_005496) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/smalt/

Software that aligns DNA sequencing reads with a reference genome. Reads from a wide range of sequencing platforms, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including paired reads.

Proper citation: SMALT (RRID:SCR_005498) Copy   

•   Source: SciCrunch Registry

http://www.enseignementsup-recherche.gouv.fr/

Ministry of Higher Education, Research and Innovation, France is one of the 900 Higher Education-related Organizations and Associations.

Proper citation: French Ministry of Higher Education and Research (RRID:SCR_005532) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.uni-leipzig.de/Software/segemehl/

A software to map short sequencer reads to reference genomes. It is able to detect not only mismatches but also insertions and deletions. Furthermore, it is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping.

Proper citation: Segemehl (RRID:SCR_005494) Copy   

•   Source: SciCrunch Registry

http://pass.cribi.unipd.it/cgi-bin/pass.pl

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 19, 2020.A program to align short sequences that has been developed with an innovative strategy to perform fast gapped and ungapped alignment onto a reference sequence. It supports several data formats and allows the user to modulate very finely the sensitivity of the alignments. The program is designed to handle huge amounts of short reads generated by ILLUMINA, SOLiD and Roche-454 technology. The optimization of the internal data structure and a filter based on precomputed short-word alignments allow the program to skip false positives in the extension phase, thus reducing the execution time without loss of sensitivity. The final alignment is performed by dynamic programming., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PASS (RRID:SCR_005490) Copy   

•   Source: SciCrunch Registry

http://www.salute.gov.it/

Governmental agency of Italy. Its headquarters are in Rome and is led by the Italian Minister of Health.

Proper citation: Ministry of Health; Rome; Italy (RRID:SCR_005526) Copy   

•   Source: SciCrunch Registry

http://pythonhosted.org/pyDNase/

A software library for analyzing DNase-seq data.

Proper citation: pyDNase (RRID:SCR_005406) Copy   

•   Source: SciCrunch Registry

http://pringlelab.stanford.edu/projects.html

Software to collapse identical and near-identical Illumina and 454 reads (such as those from PCR clones) into single error-corrected sequences; it can process paired-end as well as single-end reads. Fulcrum is customizable and can be deployed on a single machine, a local network or a commercially available MapReduce cluster, and it has been optimized to maximize ease-of-use, cross-platform compatibility and future scalability. Sequence datasets have been collapsed by up to 71%, and the reduced number and improved quality of the resulting sequences allow assemblers to produce longer contigs while using less memory.

Proper citation: Fulcrum (RRID:SCR_005523) Copy   

•   Source: SciCrunch Registry

http://www.randox.com/

An Antibody supplier

Proper citation: Randox Life Sciences (RRID:SCR_005525) Copy   

•   Source: SciCrunch Registry

http://maq.sourceforge.net/

A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way.

Proper citation: Maq (RRID:SCR_005485) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/mosaik-aligner/

A reference-guided assembler comprising of two main modular programs: MosaikBuild and MosaikAligner. MosaikBuild converts various sequence formats into Mosaik?s native read format. MosaikAligner pairwise aligns each read to a specified series of reference sequences and produces BAMs as outputs. At this time, the workflow consists of supplying sequences in FASTA, FASTQ, Illumina Bustard & Gerald, or SRF file formats and producing results in the BAM format. Unlike many current read aligners, MOSAIK produces gapped alignments using the Smith-Waterman algorithm. MOSAIK is written in highly portable C++ and currently targetted for the following platforms: Microsoft Windows, Apple Mac OS X, FreeBSD, and Linux operating systems. Other platforms can easily be supported upon request. MOSAIK is multithreaded. If you have a machine with 8 processors, you can use all 8 processors to align reads faster while using the same memory footprint as when using one processor. MOSAIK supports multiple sequencing technologies. In addition to legacy technologies such as Sanger capillary sequencing, our program supports next generation technologies such as Roche 454, Illumina, AB SOLiD, and experimental support for the Helicos Heliscope.

Proper citation: MOSAIK (RRID:SCR_005486) Copy   

•   Source: SciCrunch Registry

http://chipexo.sourceforge.net/

A bioinformatics tool dedicated to analyze ChIP-exo data: 1) Sequencing depth normalization and nucleotide composition bias correction. 2) Signal consolidation and noise reduction. 3) Single base resolution border detection. 4) Border matching.

Proper citation: MACE (RRID:SCR_005520) Copy   

•   Source: SciCrunch Registry

http://cibiv.github.io/NextGenMap/

A mapping program for Next Generation Sequencing reads that is more than twice as fast as BWA, while achieving a mapping sensitivity similar to Stampy or Bowtie2. NextGenMap uses a memory efficient index structure (hash table) to store the positions of all 13-mers present in the reference genome. This index enables a quick identification of potential mapping regions for every read. Unlike other methods, NextGenMap dynamically determines for each read individually how many of the potential mapping regions have to be evaluated by a pairwise sequence alignment. Moreover, NextGenMap uses fast SIMD instructions (SSE) to accelerate the alignment calculations on the CPU. If available NextGenMap calculates the alignments on the GPU (using OpenCL/CUDA) resulting in a runtime reduction of another 20 - 50 %, depending on the underlying data set.

Proper citation: NextGenMap (RRID:SCR_005488) Copy   

•   Source: SciCrunch Registry