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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Flexbar Resource Report Resource Website 100+ mentions |
Flexbar (RRID:SCR_013001) | Flexbar | software resource | Flexible barcode and adapter removal for sequencing platforms. | bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
DOI:10.3390/biology1030895 | biotools:flexbar | https://bio.tools/flexbar, https://sources.debian.org/src/flexbar/ | SCR_013001 | 2026-07-25 12:07:43 | 281 | |||||||
|
LOCAS Resource Report Resource Website 1+ mentions |
LOCAS (RRID:SCR_013064) | LOCAS | software resource | A software to assemble short reads of next generation sequencing technologies at low coverage. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21858125 | OMICS_00019, biotools:locas | https://bio.tools/locas | SCR_013064 | 2026-07-25 12:07:45 | 2 | |||||||
|
PRICE Resource Report Resource Website 100+ mentions |
PRICE (RRID:SCR_013063) | PRICE | software resource | Software for a de novo genome assembler implemented in C++. | c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at San Francisco; California; USA |
OMICS_01430, biotools:price | https://bio.tools/price | SCR_013063 | Paired-Read Iterative Contig Extension | 2026-07-25 12:07:43 | 162 | |||||||
|
OntoQuest Resource Report Resource Website |
OntoQuest (RRID:SCR_013281) | OntoQuest | software resource | An ontology management module to perform ontology-based search over data sources. This management system permits a user to store, search and navigate any number of OWL-structured ontologies. Ontoquest may also be accessed through a variety of web services via the Neuroscience Information Framework. | ontology, interoperability, owl, middleware, web service, bio.tools, bio.tools |
is listed by: 3DVC is listed by: bio.tools is listed by: Debian is related to: NIFSTD is related to: NIF Web Services has parent organization: Neuroscience Information Framework |
PMID:18958629 | biotools:list_ontologies, biotools:ontoquest_ws, nlx_151737 | https://bio.tools/list_ontologies, https://bio.tools/ontoquest_ws | SCR_013281 | Ontoquest | 2026-07-25 12:07:49 | 0 | ||||||
|
RDXplorer Resource Report Resource Website 1+ mentions |
RDXplorer (RRID:SCR_013290) | RDXplorer | software resource | A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
biotools:RDXplorer, OMICS_00349 | https://bio.tools/RDXplorer | SCR_013290 | 2026-07-25 12:07:47 | 7 | ||||||||
|
CEM Resource Report Resource Website 1+ mentions |
CEM (RRID:SCR_013241) | CEM | software resource | An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Riverside; California; USA |
OMICS_01271, biotools:cem | https://bio.tools/cem | SCR_013241 | CEM: Transcriptome Assembly and Isoform Expression Level Estimation from Biased RNA-Seq Reads | 2026-07-25 12:07:48 | 1 | |||||||
|
BEADS Resource Report Resource Website 10+ mentions |
BEADS (RRID:SCR_013229) | BEADS | software resource | Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:21646344 | OMICS_00466, biotools:beads | https://bio.tools/beads | SCR_013229 | BEADS: Bias Elimination Algorithm for Deep Sequencing, Bias Elimination Algorithm for Deep Sequencing | 2026-07-25 12:07:46 | 37 | ||||||
|
Trans-ABySS Resource Report Resource Website 50+ mentions |
Trans-ABySS (RRID:SCR_013322) | Trans-ABySS | software resource | A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
OMICS_01326, biotools:trans-abyss | https://bio.tools/trans-abyss/ | SCR_013322 | 2026-07-25 12:07:52 | 69 | ||||||||
|
chimerascan Resource Report Resource Website 50+ mentions |
chimerascan (RRID:SCR_013298) | chimerascan | software resource | Software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets. Used for detection of chimeric transcripts in high-throughput sequencing data. | Gene fusion detection, paired-end RNA sequencing data, RNA sequencing data, chimeric transcripts detection, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:chimerascan, OMICS_01343 | https://bio.tools/chimerascan | SCR_013298 | 2026-07-25 12:07:47 | 53 | |||||||
|
Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers Resource Report Resource Website 1+ mentions |
Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers (RRID:SCR_013409) | PCS | software resource | A stand-alone package to identify and analyze conserved k-mers in pairwise alignment. This program shows high performance for identifying miRNA seed binding sites in 3''-UTRs. | perl, perl script, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Tsinghua University; Beijing; China |
biotools:pcs, nlx_33020 | https://bio.tools/pcs | http://bioinfo.au.tsinghua.edu.cn/member/~gujin/pcs/ | SCR_013409 | Pairwise Conservation Scores | 2026-07-25 12:07:49 | 3 | ||||||
|
TreeView Resource Report Resource Website 1000+ mentions |
TreeView (RRID:SCR_013503) | TreeView | software resource | Software to graphically browse results of clustering and other analyses from Cluster. |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
DOI:10.1093/bioinformatics/bth349 | OMICS_01574 | https://sources.debian.org/src/treeview/ | SCR_013503 | 2026-07-25 12:07:54 | 2742 | ||||||||
|
CNV-seq Resource Report Resource Website 100+ mentions |
CNV-seq (RRID:SCR_013357) | CNV-seq | software resource | A method for detecting DNA copy number variation (CNV) using high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:cnv-seq, OMICS_00339 | https://bio.tools/cnv-seq | SCR_013357 | 2026-07-25 12:07:50 | 167 | |||||||
|
Integrative Genomics Viewer Resource Report Resource Website 500+ mentions |
Integrative Genomics Viewer (RRID:SCR_011793) | IGV | software resource | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. | genomic datasets exploration, |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
DOI:10.1038/nbt.1754 | OMICS_00917, biotools:igv | https://bio.tools/igv, https://sources.debian.org/src/igv/ | SCR_011793 | 2026-07-25 12:07:22 | 809 | |||||||
|
NCBI Genome Workbench Resource Report Resource Website 10+ mentions |
NCBI Genome Workbench (RRID:SCR_011794) | Genome Workbench | software resource | An integrated application for viewing and analyzing sequence data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
OMICS_00920, biotools:ncbi_genome_workbench | https://bio.tools/ncbi_genome_workbench | SCR_011794 | 2026-07-25 12:07:24 | 11 | ||||||||
|
ngs.plot Resource Report Resource Website 10+ mentions |
ngs.plot (RRID:SCR_011795) | ngs.plot | software resource | A software program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions. | bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
GNU General Public License, v3 | BioTools:ngs.plot, OMICS_00922, biotools:ngs.plot | https://bio.tools/ngs.plot, https://bio.tools/ngs.plot, https://bio.tools/ngs.plot | SCR_011795 | ngsplot, ngsplot - Quick mining and visualization of next-generation sequencing data by integrating genomic databases | 2026-07-25 12:07:20 | 42 | ||||||
|
MizBee Resource Report Resource Website 1+ mentions |
MizBee (RRID:SCR_011804) | MizBee | software resource | A multiscale synteny browser for exploring conservation relationships in comparative genomics data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Utah; Utah; USA |
OMICS_00943, biotools:mizbee | https://bio.tools/mizbee | SCR_011804 | MizBee - A Multiscale Synteny Browser | 2026-07-25 12:07:24 | 2 | |||||||
|
ConDeTri Resource Report Resource Website 50+ mentions |
ConDeTri (RRID:SCR_011838) | ConDeTri | software resource | Software tool as content dependent read trimmer for Illumina data. Content dependent read trimming software for Illumina/Solexa sequencing data. | Solexa sequencing data, Illumina data, data read trimming, read trimmer, sequencing data, |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22039460 | Free, Available for download, Freely available | OMICS_01085, biotools:condetri | https://bio.tools/condetri, https://sources.debian.org/src/condetri/, https://github.com/linneas/condetri/ | SCR_011838 | 2026-07-25 12:07:21 | 66 | ||||||
|
Circos Resource Report Resource Website 5000+ mentions |
Circos (RRID:SCR_011798) | Circos | software resource | A software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: JupiterPlot |
DOI:10.1101/gr.092759.109 | biotools:circos, OMICS_00932 | https://bio.tools/circos, https://sources.debian.org/src/circos/ | SCR_011798 | 2026-07-25 12:07:24 | 5084 | |||||||
|
AlienTrimmer Resource Report Resource Website 50+ mentions |
AlienTrimmer (RRID:SCR_011835) | AlienTrimmer | software resource | Allows detecting and removing multiple alien sequences in both ends of sequence reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23912058 | Free | biotools:alientrimmer, OMICS_01082 | https://bio.tools/alientrimmer | SCR_011835 | 2026-07-25 12:07:21 | 68 | ||||||
|
Scythe Resource Report Resource Website 100+ mentions |
Scythe (RRID:SCR_011844) | Scythe | software resource | Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. |
is listed by: OMICtools is listed by: Debian |
OMICS_01091 | https://sources.debian.org/src/scythe/ | SCR_011844 | Scythe - A Bayesian adapter trimmer | 2026-07-25 12:07:21 | 174 |
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