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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PeakSeq Resource Report Resource Website 10+ mentions |
PeakSeq (RRID:SCR_005349) | PeakSeq | software resource | 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. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Yale University; Connecticut; USA |
PMID:19122651 | biotools:peakseq, OMICS_00453 | https://bio.tools/peakseq | SCR_005349 | 2026-09-19 12:50:52 | 39 | |||||||
|
Anne O'Tate Resource Report Resource Website 1+ mentions |
Anne O'Tate (RRID:SCR_005340) | Anne O'Tate | service resource | 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. | database |
is listed by: OMICtools is related to: PubMed has parent organization: University of Illinois at Chicago; Illinois; USA |
PMID:18279519 | OMICS_01171 | SCR_005340 | 2026-09-19 12:50:51 | 2 | ||||||||
|
GEM Resource Report Resource Website 10+ mentions |
GEM (RRID:SCR_005339) | GEM | software resource | 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. | chip-seq, chip-exo, genome, event, motif, protein-dna interaction, java, transcription factor, genome sequence, motif discovery, binding event calling |
is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
PMID:22912568 | OMICS_00441 | SCR_005339 | Genome wide Event finding and Motif discovery, GEM: ChIP-Seq and ChIP-exo analysis tool | 2026-09-19 12:50:51 | 12 | |||||||
|
Hiclib Resource Report Resource Website 10+ mentions |
Hiclib (RRID:SCR_005535) | Hiclib | software resource | An Software resource | is listed by: OMICtools | OMICS_00521 | SCR_005535 | 2026-09-19 12:50:55 | 22 | ||||||||||
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SHRiMP Resource Report Resource Website 100+ mentions |
SHRiMP (RRID:SCR_005496) | SHRiMP | software resource | A software package for aligning genomic reads against a target genome. | next generation sequencing, alignment |
is used by: Jambalaya is listed by: OMICtools is related to: Jambalaya is related to: Proovread has parent organization: University of Toronto; Ontario; Canada |
PMID:21278192 | OMICS_00685 | SCR_005496 | SHRiMP - SHort Read Mapping Package | 2026-09-19 12:50:54 | 208 | |||||||
|
SMALT Resource Report Resource Website 500+ mentions |
SMALT (RRID:SCR_005498) | SMALT | software resource | 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. |
is listed by: OMICtools is related to: Sequence Search and Alignment by Hashing Algorithm has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
OMICS_00686 | SCR_005498 | 2026-09-19 12:50:54 | 516 | ||||||||||
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TIGRFAMS Resource Report Resource Website 100+ mentions |
TIGRFAMS (RRID:SCR_005493) | JCVI TIGRFAMS, TIGRFAM | data or information resource, data set, database | Consists curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. Starting with release 10.0, TIGRFAMs models use HMMER3, which provides excellent search speed as well as exquisite search sensitivity. See the "TIGRFAMs Complete Listing" page to review the accession, protein name, model type, and EC number (if assigned) of all models. TIGRFAMs is a member database in InterPro. The HMM libraries and supporting files are available to download and use for free from our FTP site. | sequence alignment, hidden markov model, protein sequence, classification, protein, protein family, sequence homology, sequence, homology, function, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: InterPro is related to: InterPro has parent organization: J. Craig Venter Institute |
PMID:23197656 | Free | nif-0000-03560, OMICS_01700, biotools:tigrfams | https://bio.tools/tigrfams | http://www.tigr.org/TIGRFAMs | SCR_005493 | TIGRFAMs | 2026-09-19 12:50:54 | 142 | ||||
|
Segemehl Resource Report Resource Website 10+ mentions |
Segemehl (RRID:SCR_005494) | Segemehl | software resource | 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. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: ANNOgesic has parent organization: University of Leipzig; Saxony; Germany |
PMID:24512684 PMID:22581174 PMID:19750212 DOI:10.1371/journal.pcbi.1000502 |
Acknowledgement requested, Free, Public | biotools:segemehl, OMICS_00683 | https://bio.tools/segemehl, https://sources.debian.org/src/segemehl/ | SCR_005494 | segemehl - short read mapping with gaps | 2026-09-19 12:50:54 | 48 | |||||
|
PASS Resource Report Resource Website 1000+ mentions |
PASS (RRID:SCR_005490) | PASS | software resource | 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. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: PASS-bis has parent organization: University of Padua; Padua; Italy |
PMID:19218350 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:pass, OMICS_00673 | https://bio.tools/pass | SCR_005490 | PASS: a program to align short sequences | 2026-09-19 12:50:54 | 2085 | |||||
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Fulcrum Resource Report Resource Website 1+ mentions |
Fulcrum (RRID:SCR_005523) | Fulcrum | software resource | 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. | illumina, 454, read, paired-end read, single-end read, high-throughput sequencing, redundant read, genome, transcriptome, ultra high throughput sequencing |
is listed by: OMICtools has parent organization: Stanford University School of Medicine; California; USA |
PMID:22419786 | BSD-like license | OMICS_01049 | http://pringlelab.stanford.edu/protocols.html | SCR_005523 | Fulcrum Read Collapser | 2026-09-19 12:50:55 | 4 | |||||
|
Maq Resource Report Resource Website 50+ mentions |
Maq (RRID:SCR_005485) | Maq | software resource | A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way. | command-line, curses/ncurses, opengl, c, c++, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
DOI:10.1101/gr.078212.108 | GNU General Public License, v2 | OMICS_00668, biotools:maq | https://bio.tools/maq, https://sources.debian.org/src/maq/ | SCR_005485 | mapass2, Mapping and Assembly with Quality, Mapping and Assembly with Qualities, Maq: Mapping and Assembly with Qualities | 2026-09-19 12:50:54 | 74 | |||||
|
MOSAIK Resource Report Resource Website 50+ mentions |
MOSAIK (RRID:SCR_005486) | MOSAIK | software resource | 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. | next-generation sequencing, alignment, smith-waterman algorithm, c++, computational biology, reference guided aligner |
is listed by: OMICtools is listed by: Debian is related to: 1000 Genomes: A Deep Catalog of Human Genetic Variation has parent organization: Google Code |
Free, Freely available | OMICS_00669 | https://sources.debian.org/src/mosaik-aligner/ | SCR_005486 | mosaik-aligner | 2026-09-19 12:50:54 | 87 | ||||||
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MACE Resource Report Resource Website 1000+ mentions |
MACE (RRID:SCR_005520) | MACE | software resource | 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. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00520 | SCR_005520 | MACE: Model based Analysis of ChIP-exo | 2026-09-19 12:50:55 | 1192 | |||||||||
|
NextGenMap Resource Report Resource Website 100+ mentions |
NextGenMap (RRID:SCR_005488) | NGM | software resource | 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. | next-generation sequencing |
is listed by: OMICtools has parent organization: University of Vienna; Vienna; Austria |
OMICS_00672 | SCR_005488 | Nextgenmap - A mapping method for Next Generation Sequencing reads | 2026-09-19 12:50:54 | 179 | ||||||||
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ea-utils Resource Report Resource Website 100+ mentions |
ea-utils (RRID:SCR_005553) | ea-utils | software resource | 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. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.2174/1875036201307010001 | MIT License | OMICS_01041, biotools:ea-utils | https://bio.tools/ea-utils, https://sources.debian.org/src/ea-utils/ | SCR_005553 | ea-utils: FASTQ processing utilities | 2026-09-19 12:50:55 | 289 | |||||
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BSeQC Resource Report Resource Website 1+ mentions |
BSeQC (RRID:SCR_005428) | BSeQC | software resource | 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. | bisulfite sequencing, bisulfite, sequencing | is listed by: OMICtools | Artistic License, GNU General Public License | OMICS_00572 | SCR_005428 | BSeQC: Quality Control of bisulfite sequencing experiments | 2026-09-19 12:50:53 | 6 | |||||||
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NGSQC Resource Report Resource Website 100+ mentions |
NGSQC (RRID:SCR_005459) | NGSQC | software resource | Software pipeline that provides a set of novel quality control measures for quickly detecting a wide variety of quality issues in deep sequencing data derived from two dimensional surfaces, regardless of the assay technology used. It also enables researchers to determine whether sequencing data related to their most interesting biological discoveries are caused by sequencing quality issues. NGSQC can help to ensure that biological conclusions, in particular those based on relatively rare sequences, are not caused by low quality sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | next generation sequencing, quality control |
is listed by: OMICtools has parent organization: University of Michigan; Ann Arbor; USA |
PMID:21143816 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01064 | SCR_005459 | Next Generation Sequencing Quality Control, NGSQC: Next Generation Sequencing Quality Control | 2026-09-19 12:50:53 | 129 | ||||||
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MSC Resource Report Resource Website |
MSC (RRID:SCR_005450) | MSC | software resource | A classification software for DNA methylation profiling with bisulphite next-generation sequencing data. | classification, dna methylation, bisulfite, next-generation sequencing, methylation, r | is listed by: OMICtools | PMID:24273245 | OMICS_00610 | SCR_005450 | Methylation Status Calling | 2026-09-19 12:50:53 | 0 | |||||||
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MLML Resource Report Resource Website 1+ mentions |
MLML (RRID:SCR_005449) | MLML | software resource | A software tool to simultaneously estimate hydroxymethylation (5hmC) and methylation (5mC) levels from BS-seq, oxBS-seq and TAB-seq experiments. It generates consistent estimates across experiment types. |
is listed by: OMICtools has parent organization: University of Southern California; Los Angeles; USA |
OMICS_00609 | SCR_005449 | 2026-09-19 12:50:53 | 7 | ||||||||||
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MethylExtract Resource Report Resource Website 10+ mentions |
MethylExtract (RRID:SCR_005446) | MethylExtract | software resource | A user friendly software tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation. | bisulfite sequencing, methylation map, methylation, sequence variation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Granada; Granada; Spain |
Acknowledgement requested | biotools:methylextract, OMICS_00605 | https://bio.tools/methylextract | SCR_005446 | High-Quality methylation maps and SNV calling from BS-Seq experiments | 2026-09-19 12:50:53 | 14 |
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