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http://www-personal.umich.edu/~jianghui/seqmap/

A software tool for mapping large amount of oligonucleotide to the genome. It is designed for finding all the places in a genome where an oligonucleotide could potentially come from. SeqMap can efficiently map as many as dozens of millions of short sequences to a genome of several billions of nucleotides. While doing the mapping, several mutations as well as insertions / deletions of the nucleotide bases in the sequences can be tolerated and furthermore detected. Various input and output formats are supported, as well as many command line options for tuning almost every steps in the mapping process. A typical mapping can be done in a few hours on an ordinary PC.

Proper citation: SeqMap (RRID:SCR_005495) Copy   

•   Source: SciCrunch Registry

http://www.genome.umd.edu/jellyfish.html

A software tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the compare-and-swap CPU instruction to increase parallelism. Jellyfish is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the jellyfish dump command., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Jellyfish (RRID:SCR_005491) Copy   

•   Source: SciCrunch Registry

https://github.com/mfumagalli/ngsTools

A collection of software programs for population genetics analyses from NGS (Next-Generation Sequencing) data, taking into account its statistical uncertainty. The methods implemented in these programs do not rely on SNP (Single Nucleotide Polymorphism) or genotype calling, and are particularly suitable for low sequencing depth data.

Proper citation: ngsTools (RRID:SCR_005489) Copy   

•   Source: SciCrunch Registry

http://mrfast.sourceforge.net/

Software designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient mannerl. Currently Supported Features: * Output in SAM format * Indels up to 8 bp (4 bp deletions and 4 bp insertions) * Paired-end mapping ** Discordant option to generate mapping file ready for VariationHunter to detect structural variants. * One end anchored (OEA) map locations for novel sequence insertion detection with NovelSeq * Matepair library mapping (long inserts with RF orientation). Planned Features: * Multithreading

Proper citation: mrFAST (RRID:SCR_005487) Copy   

•   Source: SciCrunch Registry

http://dna.cs.byu.edu/gnumap/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. A software program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. By using the posterior probability of mapping a given read to a specific genomic loation, we are able to account for repetitive reads by distributing them across several regions in the genome. In addition, the output of the program is created in such a way that it can be easily viewed through other free and readily- available programs. Several benchmark data sets were created with spiked-in duplicate regions, and GNUMAP was able to more accurately account for these duplicate regions.

Proper citation: GNUMAP (RRID:SCR_005482) Copy   

•   Source: SciCrunch Registry

http://samstat.sourceforge.net/

C software program for displaying sequence statistics for next generation sequencing. Works with large fasta, fastq and SAM/BAM files.

Proper citation: SAMStat (RRID:SCR_005432) Copy   

•   Source: SciCrunch Registry

http://solexaqa.sourceforge.net/

Software package to calculate sequence quality statistics and create visual representations of data quality for Illumina's second-generation sequencing technology.

Proper citation: SolexaQA (RRID:SCR_005421) Copy   

•   Source: SciCrunch Registry

http://dna.leeds.ac.uk/methylviewer/

A simple integrated software tool for handling MAP (methyltransferase accessibility protocol) and MAP-IT (MAP individual templates) footprinting projects. It can process sequence data (*.txt, *.ab1 and *.scf) derived from the use of up to four different DNA methyltransferases.

Proper citation: MethylViewer (RRID:SCR_005448) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.babraham.ac.uk/projects/hicup/

A tool for mapping and performing quality control on Hi-C data.

Proper citation: HiCUP (RRID:SCR_005569) Copy   

•   Source: SciCrunch Registry

http://epigenome.usc.edu/publicationdata/bissnp2011/

A software package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq, RRBS and any other bisulfite treated sequencing) with Illumina directional library protocol. It contains the following key features: * Call and summarize methylation of any cytosine context provided (CpG, CHH, CHG, GCH et.al.); * Work for single end and paired-end data; * Accurtae variant detection. Enable base quality recalibration and indel calling in bisulfite sequencing; * Based on Java map-reduce framework, allow multi-thread computing. Cross-platform; * Allow multiple output format, detailed VCF files, CpG haplotype reads file for mono-allelic methylation analysis, simplified bedGraph, wig and bed format for visualization in UCSC genome broswer and IGV browser. BisSNP uses bayesian inference with locus specific methylation probabilities and bisulfite conversion rate of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Bis-SNP (RRID:SCR_005439) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/distmap/

A user-friendly software pipeline designed to map short reads in a MapReduce framework on a local Hadoop cluster. It is designed to be easily implemented by researchers who do not have expert knowledge of bioinformatics. As it does not have any dependencies, it provides full flexibility and control to the user. The user can use any version of a compatible mapper and any reference genome assembly. There is no need to maintain the mapper, reference or DistMap source code on each of the slaves (nodes) in the Hadoop cluster, making maintenance extremely easy.

Proper citation: DistMap (RRID:SCR_005473) Copy   

•   Source: SciCrunch Registry

http://www.well.ox.ac.uk/project-stampy

A software package for the mapping of short reads from illumina sequencing machines onto a reference genome. It''s recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation relative to the reference, in particular for those containing insertions or deletions. It can map reads from a highly divergent species to a reference genome for instance. Stampy achieves high sensitivity and speed by using a fast hashing algorithm and a detailed statistical model. Stampy has the following features: * Maps single, paired-end and mate pair Illumina reads to a reference genome * Fast: about 20 Gbase per hour in hybrid mode (using BWA) * Low memory footprint: 2.7 Gb shared memory for a 3Gbase genome * High sensitivity for indels and divergent reads, up to 10-15% * Low mapping bias for reads with SNPs * Well calibrated mapping quality scores * Input: Fastq and Fasta; gzipped or plain * Output: SAM, Maq''s map file * Optionally calculates per-base alignment posteriors * Optionally processes part of the input * Handles reads of up to 4500 bases

Proper citation: Stampy (RRID:SCR_005504) Copy   

•   Source: SciCrunch Registry

http://ngsview.sourceforge.net/

A generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface.

Proper citation: NGSView (RRID:SCR_005637) Copy   

•   Source: SciCrunch Registry

http://sybil.sourceforge.net/

A web-based software package for comparative genomics.

Proper citation: Sybil (RRID:SCR_005593) Copy   

•   Source: SciCrunch Registry

http://zhanglab.c2b2.columbia.edu/index.php/OLego

A program specifically designed for de novo spliced mapping of mRNA-seq reads. It adopts a multiple-seed-and-extend scheme, and does not rely on a separate external mapper.

Proper citation: OLego (RRID:SCR_005811) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/pepr-chip-seq/

A ChIP-Seq peak calling or differential binding analysis tool that is primarily designed for data with biological replicates. It uses a negative binomial distribution to model the read counts among the samples in the same group, and look for consistent differences between ChIP and control group or two ChIP groups run under different conditions.

Proper citation: PePr (RRID:SCR_005759) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.uni-freiburg.de/Software/GraphProt/

Software for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete.

Proper citation: GraphProt (RRID:SCR_005842) Copy   

•   Source: SciCrunch Registry

http://www.clipz.unibas.ch/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets.

Proper citation: CLIPZ (RRID:SCR_005755) Copy   

•   Source: SciCrunch Registry

http://europepmc.org/

Free access to biomedical literature resources including all of PubMed and PubMed Central, agricultural abstracts (from AGRICOLA), over 4 million international life science patents abstracts, National Health Service (NHS) clinical guidelines, and is supplemented with Chinese Biological Abstracts and the Citeseer database. As well as powerful search of abstracts and full text articles, it also includes: * article citations and sort order based on citation count * data citations mined from full text articles * links to and from related databases and institutional repositories * a tool to create bibliographies linked to your ORCID * named entity recognition of keywords and text-mining-based applications showcased in Europe PMC Labs * Tools for recipients of grants from one of the Europe PMC funders to deposit full-text manuscripts and link them to those specific grants. * Web services for programmatic access to all the above bibliographic information and 50,000 grants. * Search by publication date, relevance, or the number of times an article has been cited. * Links to public databases such as UniProt, Protein Data Bank (PDBe), and the European Nucleotide Archive (ENA) are provided. * Through textmining technologies, you can highlight and browse keywords such as gene names, organisms and diseases. * Search 40,000 biomedical research grants awarded to the 18,000 PIs supported by the Europe PMC funders. * Roadtest new tools based on Europe PMC content in Europe PMC labs. * In Europe PMC plus, PIs supported by the Europe PMC funders can link grants to publication information, view article citation and download statistics, and submit manuscripts.

Proper citation: Europe PubMed Central (RRID:SCR_005901) Copy   

•   Source: SciCrunch Registry

http://www-math.u-strasbg.fr/genpred/spip.php?article3

R software package to study, predict and simulate the diffusion of a signal through a temporal gene network. It predicts changes in gene expressions after a biological perturbation in the network and provides graphical outputs that allow monitoring the spread of a signal through the network., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Cascade (RRID:SCR_005861) Copy   

•   Source: SciCrunch Registry