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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Randox Life Sciences Resource Report Resource Website 1+ mentions |
Randox Life Sciences (RRID:SCR_005525) | commercial organization | An Antibody supplier | nlx_152446 | SCR_005525 | Randox Laboratories Ltd. | 2026-08-01 12:02:54 | 7 | |||||||||||
|
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 | biotools:maq, OMICS_00668 | 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 | 2026-08-01 12:02:59 | 69 | |||||
|
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 | 2026-08-01 12:02:53 | 86 | ||||||
|
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 | 2026-08-01 12:03:00 | 1172 | |||||||||
|
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 | 2026-08-01 12:02:59 | 167 | ||||||||
|
RayBiotech Resource Report Resource Website 5000+ mentions |
RayBiotech (RRID:SCR_005517) | commercial organization | An Antibody supplier | nlx_152447, Wikidata: Q30296336, grid.452664.7 | https://ror.org/026djmp70 | SCR_005517 | RayBiotech Inc., RayBiotech Inc | 2026-08-01 12:03:00 | 5475 | ||||||||||
|
Ministry of Education and Science of the Russian Federation Resource Report Resource Website 1+ mentions |
Ministry of Education and Science of the Russian Federation (RRID:SCR_005434) | government granting agency | SCR_005434 | Russian Ministry of Education and Science | 2026-08-01 12:02:59 | 4 | |||||||||||||
|
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 | 2026-08-01 12:03:00 | 282 | |||||
|
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 | 2026-08-01 12:02:52 | 6 | |||||||
|
University of Liverpool; Liverpool; United Kingdom Resource Report Resource Website 1+ mentions |
University of Liverpool; Liverpool; United Kingdom (RRID:SCR_005424) | university | 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. |
uses: ShareLaTeX is related to: Predict-TB is related to: MIP-DILI is related to: ShareLaTeX is parent organization of: Liverpool Tissue Bank is parent organization of: Human Ageing Genomic Resources is parent organization of: Digital Ageing Atlas is parent organization of: Predict-TB is parent organization of: Dietary Restriction Gene Database is parent organization of: ConPlot is parent organization of: University of Liverpool Egg Facility (LIV-SRF) is parent organization of: University of Liverpool GeneMill Core Facility is parent organization of: University of Liverpool High Field Nuclear Magnetic Resonance Core Facility is parent organization of: University of Liverpool Centre for Preclinical Imaging Core Facility is parent organization of: University of Liverpool Shared Research Histology Core Facility is parent organization of: University of Liverpool Centre for Genomic Research Core Facility is parent organization of: Liverpool University Biobank Core Facility is parent organization of: University of Liverpool Micro-X-ray-CT Shared Research Core Facility |
nlx_50695, Crossref funder ID:501100000836, grid.10025.36, ISNI:0000 0004 1936 8470, Wikidata:Q499510 | https://ror.org/04xs57h96 | SCR_005424 | University of Liverpool | 2026-08-01 12:02:52 | 1 | |||||||||
|
International Agency for Research on Cancer Resource Report Resource Website 1000+ mentions |
International Agency for Research on Cancer (RRID:SCR_005422) | IARC | nonprofit organization | 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. | cancer, human, research, prevention, carcinogenesis |
has parent organization: World Health Organization is parent organization of: IARC Recommendations and Protocols for Biobanking is parent organization of: IARC TP53 Database is parent organization of: Cancer Genomics of the Kidney (CAGEKID) |
Crossref funder ID: 100008700, grid.17703.32, ISNI: 405980095, nlx_144517, Wikidata: Q552168 | https://ror.org/00v452281 | SCR_005422 | IARC - International Agency for Research on Cancer | 2026-08-01 12:02:59 | 2163 | |||||||
|
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 | 2026-08-01 12:02:59 | 129 | ||||||
|
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 | 2026-08-01 12:02:52 | 6 | ||||||||||
|
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 | 2026-08-01 12:02:52 | 14 | ||||||
|
GobyWeb Resource Report Resource Website 1+ mentions |
GobyWeb (RRID:SCR_005443) | GobyWeb | software resource | Web application that facilitates the management and analysis of high-throughput sequencing (HTS) data. In the back-end, it uses the Goby framework, BWA, STAR, Last, GSNAP, Samtools, VCF-tools, along with a cluster of servers to provide rapid alignment and efficient analyses. GobyWeb makes it possible to analyze hundreds of samples in consistent ways without having to use command line tools. GobyWeb provides tools that streamline frequent data analyses for RNA-Seq, Methyl-Seq, RRBS, or DNA-Seq datasets and to enable teams of investigators to share reads and results of analyses. GobyWeb can be extended for new analyses by developing plugins. | high-throughput sequencing, gene expression, dna methylation, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Weill Cornell Medical College; New York; USA |
PMID:23936070 | Acknowledgement requested, GNU Lesser General Public License, v3 | OMICS_00601, biotools:gobyweb | https://bio.tools/gobyweb | SCR_005443 | 2026-08-01 12:02:59 | 3 | ||||||
|
QC-Chain Resource Report Resource Website 1+ mentions |
QC-Chain (RRID:SCR_005438) | QC-Chain | software resource | A software package of quality control tools for next generation sequencing (NGS) data, consisting of both raw reads quality evaluation and de novo contamination screening, which could identify all possible contamination sequences. This QC pipeline supplies a fast, easy-to-use, and parallel processing approach to accomplish the comprehensive QC steps, which could be applied widely to almost all kinds of NGS reads, including genomic, transcriptomic and metagenomic data. | next generation sequencing |
is listed by: OMICtools has parent organization: Chinese Academy of Sciences; Beijing; China |
OMICS_01070 | SCR_005438 | 2026-08-01 12:02:54 | 4 | |||||||||
|
VDJ Resource Report Resource Website 1+ mentions |
VDJ (RRID:SCR_005475) | software resource | Python package for analysing immune receptor sequences (antibodies and T cell receptors). | standalone software, python | is listed by: OMICtools | PMID:24639495 | Apache License, v2 | OMICS_04064 | SCR_005475 | 2026-08-01 12:02:54 | 3 | ||||||||
|
CASHX Resource Report Resource Website 1+ mentions |
CASHX (RRID:SCR_005477) | CASHX | software resource | Software pipeline to parse, map, quantify and manage large quantities of sequence data. CASHX is a set of tools that can be used together, or as independent modules on their own. The reference genome alignment tools can be used with any reference sequence in fasta format. The pipeline was designed and tested using Arabidopsis thaliana small RNA reads generated using an Illumina 1G. |
is listed by: OMICtools has parent organization: Oregon State University; Oregon; USA |
NSF MCB-1231726; NIAI AI43288 |
PMID:19307293 | OMICS_00655 | SCR_005477 | Cache ASsisted Hash Search with Xor logic Pipeline, CASHX Pipeline, Cache ASsisted Hash Search with Xor logic | 2026-08-01 12:02:53 | 4 | |||||||
|
DiProGB Resource Report Resource Website 1+ mentions |
DiProGB (RRID:SCR_005651) | DiProGB | software resource | Genome browser that encodes the genome sequence by physico-chemical dinucleotide properties such as stacking energy, melting temperature or twist angle. Analyses can be performed for the + and ?, as well as for the double strand. | genome, browser, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Dinucleotide Property Database |
PMID:19605418 | Free, Freely available | biotools:diprogb, OMICS_00880 | https://bio.tools/diprogb | SCR_005651 | DiProGB - The Dinucleotide Properties Genome Browser, Dinucleotide Properties Genome Browser | 2026-08-01 12:02:57 | 4 | |||||
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MagicViewer Resource Report Resource Website 10+ mentions |
MagicViewer (RRID:SCR_005648) | MagicViewer | software resource | Software to easily visualize the short reads alignment, identify the genetic variation and associate with the annotation information of reference genome. MagicViewer provides a user-friendly interface in which large-scale short reads and sequencing depth can be easily visualized in zoomable images under user definable color scheme through an operating system-independent manner with the implement of Java language. Meanwhile, it holds a versatile genetic variation annotation and visualization interface, providing details of the query options, functional classifications, subset selection, sequence association and primer design. | dna methylation, bisulfite sequencing |
is listed by: OMICtools has parent organization: Wenzhou Medical University; Zhejiang; China |
PMID:20444865 | Free, Public | OMICS_00887 | SCR_005648 | MagicViewer: Integrated Solution for Next-generation Sequencing Data Visualization and Genetic Variation Detection and Annotation | 2026-08-01 12:02:57 | 16 |
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