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http://compbio.cs.toronto.edu/shrimp/
A software package for aligning genomic reads against a target genome.
Proper citation: SHRiMP (RRID:SCR_005496) Copy
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
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
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
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.
Proper citation: PASS (RRID:SCR_005490) Copy
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
http://pythonhosted.org/pyDNase/
A software library for analyzing DNase-seq data.
Proper citation: pyDNase (RRID:SCR_005406) Copy
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
An Antibody supplier
Proper citation: Randox Life Sciences (RRID:SCR_005525) Copy
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
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
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
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
Proper citation: Ministry of Education and Science of the Russian Federation (RRID:SCR_005434) Copy
http://www.gis.a-star.edu.sg/internet/site/
Proper citation: Genome Institute of Singapore; Singapore; Singapore (RRID:SCR_005556) Copy
http://code.google.com/p/ea-utils/
Command-line software tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.
Proper citation: ea-utils (RRID:SCR_005553) Copy
http://code.google.com/p/bseqc/
A quality control software package specially for bisulfite sequencing experiments. It can comprehensively evaluate the quality of BS-seq experiments and automatically trim nucleotides with potential technical biases. In addition, BSeQC also support removing duplicate reads and keeping one copy of the overlapping segment in paired-end sequencing.
Proper citation: BSeQC (RRID:SCR_005428) Copy
Public university based in the city of Liverpool, England. Founded as a college in 1881, it gained its Royal Charter in 1903 with the ability to award degrees and is also known to be one of the six original 'red brick' civic universities.
Proper citation: University of Liverpool; Liverpool; United Kingdom (RRID:SCR_005424) Copy
The International Agency for Research on Cancer (IARC) is part of the World Health Organization. IARC''s mission is to coordinate and conduct research on the causes of human cancer, the mechanisms of carcinogenesis, and to develop scientific strategies for cancer prevention and control. The Agency is involved in both epidemiological and laboratory research and disseminates scientific information through publications, meetings, courses, and fellowships.
Proper citation: International Agency for Research on Cancer (RRID:SCR_005422) Copy
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