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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MethylViewer Resource Report Resource Website 1+ mentions |
MethylViewer (RRID:SCR_005448) | MethylViewer | software resource | 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. | primer design, bisulfite sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Leeds; West Yorkshire; United Kingdom |
PMID:20959287 | OMICS_00608, biotools:methylviewer | https://bio.tools/methylviewer | SCR_005448 | 2026-09-19 12:50:53 | 2 | |||||||
|
HiCUP Resource Report Resource Website 100+ mentions |
HiCUP (RRID:SCR_005569) | HiCUP | software resource | A tool for mapping and performing quality control on Hi-C data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Babraham Institute |
OMICS_00523, biotools:hicup | https://bio.tools/hicup | SCR_005569 | Hi-C User Pipeline | 2026-09-19 12:50:55 | 317 | |||||||
|
Bisulfighter Resource Report Resource Website 1+ mentions |
Bisulfighter (RRID:SCR_005440) | Bisulfighter | software resource | A software package for detecting methylated cytosines (mCs) and differentially methylated regions (DMRs) from bisulfite sequencing data. | bisulfighter, python |
is listed by: OMICtools has parent organization: Google Code has parent organization: National Institute of Advanced Industrial Science and Technology |
Open unspecified license | OMICS_00593 | SCR_005440 | bisulfighter - A pipeline for accurate detection of methylated cytosines and differentially methylated regions | 2026-09-19 12:50:53 | 4 | |||||||
|
Bis-SNP Resource Report Resource Website 50+ mentions |
Bis-SNP (RRID:SCR_005439) | Bis-SNP | software resource | 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. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Southern California; Los Angeles; USA |
PMID:22784381 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:bis-snp, OMICS_00591 | https://bio.tools/bis-snp | SCR_005439 | Bis-SNP - A bisulfite space genotyper & methylation caller, Bis-SNP - A bisulfite space genotyper and methylation caller | 2026-09-19 12:50:53 | 50 | |||||
|
CUSHAW Resource Report Resource Website 1+ mentions |
CUSHAW (RRID:SCR_005479) | CUSHAW | software resource | Software package for next-generation sequencing read alignment that is fast and parallel gapped read alignment to large genomes, such as the human genome. | next-generation sequencing, read alignment, genome, alignment |
is listed by: OMICtools is related to: CUSHAW2-GPU has parent organization: Johannes Gutenberg University Mainz; Rhineland-Palatinate; Germany has parent organization: SourceForge |
PMID:22576173 PMID:24466273 |
OMICS_00658 | SCR_005479 | CUSHAW2, CUSHAW3 | 2026-09-19 12:50:54 | 2 | |||||||
|
IdCheck Resource Report Resource Website 1+ mentions |
IdCheck (RRID:SCR_005510) | IDCheck | software resource | Software that allows assessment of concordance between genotype (from SNP arrays or DNA sequencing) and gene expression (RNA-seq) samples. IDCheck compares the identity of RNA-seq reads and SNP genotypes using a likelihood based method. Based on maximum likelihood estimates of relevant parameters, we can detect sample contamination and identify correct sample pairs when swapping occurs. |
is listed by: OMICtools has parent organization: Harvard T.H. Chan School of Public Health |
OMICS_01054 | SCR_005510 | IdCheck: A tool for genotype and gene expression sample identity checking | 2026-09-19 12:50:54 | 1 | |||||||||
|
DistMap Resource Report Resource Website 10+ mentions |
DistMap (RRID:SCR_005473) | DistMap | software resource | 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. | mapreduce/hadoop, command line, hadoop cluster, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Veterinary Medicine Vienna; Vienna; Austria has parent organization: Google Code |
PMID:24009693 | GNU General Public License, v3 | OMICS_00660, biotools:distmap | https://bio.tools/distmap | SCR_005473 | 2026-09-19 12:50:54 | 23 | ||||||
|
Stampy Resource Report Resource Website 100+ mentions |
Stampy (RRID:SCR_005504) | Stampy | software resource | 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 | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Wellcome Trust Centre for Human Genetics |
PMID:20980556 | OMICS_00691, biotools:stampy | https://bio.tools/stampy | SCR_005504 | 2026-09-19 12:50:54 | 184 | |||||||
|
Scalable Nucleotide Alignment Program Resource Report Resource Website 100+ mentions |
Scalable Nucleotide Alignment Program (RRID:SCR_005501) | SNAP | software resource | A sequence aligner software program that is 10-100x faster and simultaneously more accurate than existing tools like BWA, Bowtie2 and SOAP2. It runs on commodity x86 processors, and supports a rich error model that lets it cheaply match reads with more differences from the reference than other tools. This gives SNAP up to 2x lower error rates than existing tools and lets it match larger mutations that they may miss. SNAP also natively reads BAM, FASTQ, or gzipped FASTQ, and natively writes SAM or BAM, with built-in sorting, duplicate marking, and BAM indexing. | windows, linux, os x |
is listed by: OMICtools is listed by: Debian has parent organization: University of California at Berkeley; Berkeley; USA |
Apache License, 2, Acknowledgement requested | OMICS_00687 | https://sources.debian.org/src/snap-aligner/ | SCR_005501 | SNAP - Scalable Nucleotide Alignment Program | 2026-09-19 12:50:54 | 124 | ||||||
|
NextClip Resource Report Resource Website 50+ mentions |
NextClip (RRID:SCR_005465) | NextClip | software resource | A software tool for analysing reads from Long Mate Pair (LMP) libraries, generating a comprehensive quality report and extracting good quality trimmed and deduplicated reads. | is listed by: OMICtools | PMID:24297520 | OMICS_01061 | SCR_005465 | NextClip - Nextera Long Mate Pair analysis and processing tool | 2026-09-19 12:50:54 | 73 | ||||||||
|
NGS QC Toolkit Resource Report Resource Website 100+ mentions |
NGS QC Toolkit (RRID:SCR_005461) | NGS QC Toolkit | software resource | A software toolkit for the quality control (QC) of next generation sequencing (NGS) data. The toolkit comprises of user-friendly stand alone tools for quality control of the sequence data generated using Illumina and Roche 454 platforms with detailed results in the form of tables and graphs, and filtering of high-quality sequence data. It also includes few other tools, which are helpful in NGS data quality control and analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | next generation sequencing | is listed by: OMICtools | PMID:22312429 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01062 | SCR_005461 | 2026-09-19 12:50:53 | 284 | |||||||
|
Consed Resource Report Resource Website 500+ mentions |
Consed (RRID:SCR_005650) | Consed | software resource | A graphical tool for sequence finishing (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence) | next-generation sequencing, graphical editor, linux, macosx, solaris, c++ |
is listed by: OMICtools has parent organization: University of Washington; Seattle; USA |
NIH ; NHGRI R01HG005710 |
PMID:23995391 PMID:9521923 |
Free for academic use, Free for non-profit use, Commercial license | OMICS_00879 | SCR_005650 | 2026-09-19 12:50:57 | 600 | ||||||
|
NGSView Resource Report Resource Website 1+ mentions |
NGSView (RRID:SCR_005637) | NGSView | software resource | 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. | next-generation sequence, alignment, edit, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
Acknowledgement requested | biotools:ngsview, OMICS_00891 | https://bio.tools/ngsview | SCR_005637 | 2026-09-19 12:50:57 | 2 | |||||||
|
BSMAP Resource Report Resource Website 100+ mentions |
BSMAP (RRID:SCR_005671) | BSMAP | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. Short reads mapping software for bisulfite sequencing reads. |
is listed by: OMICtools has parent organization: Google Code |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00579 | SCR_005671 | Bisulfite Sequence Mapping Program | 2026-09-19 12:50:57 | 355 | ||||||||
|
WebArrayDB Resource Report Resource Website 1+ mentions |
WebArrayDB (RRID:SCR_005577) | WebArrayDB | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, software resource, storage service resource | An open source integrated microarray database and analysis suite that features convenient uploading of data for storage in a MIAME (Minimal Information about a Microarray Experiment) compliant fashion. It allows data to be mined with a large variety of R-based tools, including data analysis across multiple platforms. Different methods for probe alignment, normalization and statistical analysis are included to account for systematic bias. Student's t-test, moderated t-tests, non-parametric tests and analysis of variance or covariance (ANOVA/ANCOVA) are among the choices of algorithms for differential analysis of data. Users also have the flexibility to define new factors and create new analysis models to fit complex experimental designs. All data can be queried or browsed through a web browser. The computations can be performed in parallel on symmetric multiprocessing (SMP) systems or Linux clusters. | is listed by: OMICtools | Prostate Cancer Foundation ; Mary Kay Ash Foundation ; NIH ; NIAI R01AI034829; NIAI R01AI052237; NCI R01CA68822; NCI U01CA114810 |
PMID:19602526 | Open source, Account required, The software package is available for the use on a public web server or can be downloaded | OMICS_00782 | SCR_005577 | 2026-09-19 12:50:56 | 8 | |||||||
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Advanced Sequence Automated Pipeline Resource Report Resource Website 100+ mentions |
Advanced Sequence Automated Pipeline (RRID:SCR_005578) | ASAP | software resource | Software developed to provide a framework for building and executing a pipeline to preprocess next generation sequence data and variant calls. | next generation sequencing |
is listed by: OMICtools has parent organization: Vanderbilt University; Tennessee; USA |
PMID:23289815 | Free | OMICS_01033 | SCR_005578 | Advanced Sequence Automated Pipeline (ASAP) | 2026-09-19 12:50:56 | 324 | ||||||
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SAMtools Text Alignment Viewer Resource Report Resource Website 1+ mentions |
SAMtools Text Alignment Viewer (RRID:SCR_005611) | SAMtools tview | software resource | Text alignment viewer software based on the GNU ncurses library that works with short indels and shows MAQ consensus. It uses different colors to display mapping quality or base quality, subjected to users' choice. | text alignment, viewer, maq consensus, indel |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00893 | SCR_005611 | Text Alignment Viewer | 2026-09-19 12:50:56 | 1 | ||||||||
|
BSmooth Resource Report Resource Website 10+ mentions |
BSmooth (RRID:SCR_005693) | BSmooth | software resource | A pipeline for analyzing whole genome bisulfite sequencing (WGBS) data. | is listed by: OMICtools | OMICS_00581 | SCR_005693 | 2026-09-19 12:50:58 | 29 | ||||||||||
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X-Tile Resource Report Resource Website 100+ mentions |
X-Tile (RRID:SCR_005602) | software resource | Software tool for biomarker assessment and outcome based cut point optimization. | biomarker assessment, outcome based cut point optimization |
is listed by: OMICtools has parent organization: Yale University; Connecticut; USA |
PMID:15534099 | Free, Available for download, Freely available | OMICS_00824 | http://www.tissuearray.org/rimmlab/xtile.html | SCR_005602 | X-tile software, X-tile | 2026-09-19 12:50:56 | 430 | ||||||
|
cancergrid-tma Resource Report Resource Website |
cancergrid-tma (RRID:SCR_005595) | cancergrid-tma | software resource | A web-based application for the management and storage of tissue microarray (TMA) images and the associated metadata. The application enables the user to navigate a grid of TMA core images within a slide, zoom and pan around an image, and enter a score constrained to a specific scoring system. The submitted scores are scored in the eXist open source database, in an XML format, which is compatible with existing TMA standards, and thus allow the data to be archived and re-used in future analysis. | tissue microarray, image |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00816 | SCR_005595 | Cancergrid Image Scorer | 2026-09-19 12:50:56 | 0 |
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