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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Vanator Resource Report Resource Website 1+ mentions |
Vanator (RRID:SCR_004370) | Vanator | software resource | A Perl pipeline utilising a large variety of common alignment, assembly and analysis tools to assess the metagenomic profiles of Illumina deep sequencing samples. The emphasis is on the discovery of novel viruses in clinical and environmental samples. | perl, metagenomic, illumina, alignment, assembly, analysis, profile, virus, clinical, environment, next-generation sequencing, taxonomy, read |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Glasgow; Glasgow; United Kingdom |
PMID:23296970 | OMICS_01505 | SCR_004370 | Vanator-CVR, Vanator-CVR - A metagenomics & virus discovery pipeline, Virus Alignment de Novo Assembly and Taxonomy On Reads, Vanator-CVR: A metagenomics and virus discovery pipeline | 2026-08-01 12:02:36 | 2 | |||||||
|
Basic OligoNucleotide Design Resource Report Resource Website 10+ mentions |
Basic OligoNucleotide Design (RRID:SCR_004492) | BOND | software resource | Software program to compute highly specific DNA oligonucleotides, for all the genes that admit unique probes, while running orders of magnitude faster than the existing programs. | dna, oligonucleotide, design, oligonucleotide design |
is listed by: OMICtools has parent organization: Western University; Ontario; Canada |
PMID:23444904 | OMICS_00827 | SCR_004492 | BOND: Basic OligoNucleotide Design | 2026-08-01 12:02:42 | 17 | |||||||
|
SOrt-ITEMS Resource Report Resource Website 1+ mentions |
SOrt-ITEMS (RRID:SCR_004716) | SOrt-ITEMS | software resource | Sequence orthology based software for improved taxonomic estimation of metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | metagenome, taxonomy, sequence, orthology, binning | is listed by: OMICtools | PMID:19439565 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01465 | SCR_004716 | Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences, SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences | 2026-08-01 12:02:44 | 6 | ||||||
|
UnifiedGenotyper Resource Report Resource Website 500+ mentions |
UnifiedGenotyper (RRID:SCR_004710) | UnifiedGenotyper | software resource | A multiple-sample, technology-aware SNP and indel caller. |
is listed by: OMICtools has parent organization: Broad Institute |
OMICS_00080 | SCR_004710 | 2026-08-01 12:02:44 | 561 | ||||||||||
|
NuChart Resource Report Resource Website 1+ mentions |
NuChart (RRID:SCR_004703) | NuChart | software resource | An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations. | is listed by: OMICtools | OMICS_00525 | SCR_004703 | 2026-08-01 12:02:39 | 2 | ||||||||||
|
Pplacer Resource Report Resource Website 10+ mentions |
Pplacer (RRID:SCR_004737) | Pplacer | software resource | Software that places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis. | classification, phylogenetic classification |
is listed by: OMICtools has parent organization: Fred Hutchinson Cancer Center |
PMID:21034504 | OMICS_01462 | SCR_004737 | pplacer: phylogenetic placement and downstream analysis | 2026-08-01 12:02:44 | 30 | |||||||
|
TETRA Resource Report Resource Website 50+ mentions |
TETRA (RRID:SCR_004573) | TETRA | software resource | Standalone software programs that can be used to calculate how well tetranucleotide usage patterns in DNA sequences correlate. Such correlations can provide valuable hints on the relatedness of DNA sequences. | tetranucleotide, dna sequence |
is listed by: OMICtools has parent organization: Max Planck Institute for Marine Microbiology; Bremen; Germany |
PMID:15305919 PMID:15507136 |
OMICS_01474 | SCR_004573 | TETRA - Fragment assignment by intrinsic tetranucleotide frequencies | 2026-08-01 12:02:42 | 67 | |||||||
|
BioPig Resource Report Resource Website 1+ mentions |
BioPig (RRID:SCR_004636) | BioPig | software resource | Software providing a framework for genomic data analysis using Apache Pig and Hadoop. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Lawrence Berkeley National Laboratory |
PMID:24021384 | biotools:biopig, OMICS_01225 | https://bio.tools/biopig | SCR_004636 | 2026-08-01 12:02:38 | 2 | |||||||
|
Nonpareil Resource Report Resource Website 50+ mentions |
Nonpareil (RRID:SCR_004629) | Nonpareil | software resource | Estimate average coverage and create Nonpareil curves for metagenomic datasets. | is listed by: OMICtools | PMID:24123672 | OMICS_01419 | SCR_004629 | 2026-08-01 12:02:43 | 83 | |||||||||
|
AbundanceBin Resource Report Resource Website 1+ mentions |
AbundanceBin (RRID:SCR_004648) | AbundanceBin | software resource | An abundance-based software tool for binning metagenomic sequences, such that the reads classified in a bin belong to species of identical or very similar abundances. AbundanceBin also gives estimations of species abundances and their genome sizes -two important characteristic parameters for a microbial community. | metagenome, sequence |
is listed by: OMICtools has parent organization: Indiana University; Indiana; USA |
PMID:21385052 | Acknowledgement requested, Free, Public | OMICS_01471 | SCR_004648 | 2026-08-01 12:02:39 | 6 | |||||||
|
INVERTER Resource Report Resource Website 1+ mentions |
INVERTER (RRID:SCR_007956) | INVERTER | software resource | Software for a de novo exact match tandem repeat finder which main advantage is without the need to specify either the pattern or a particular pattern size, integrated with a data visualization tool and has a built-in user-friendly Graphical User Interface. | is listed by: OMICtools | OMICS_00108 | SCR_007956 | 2026-08-01 12:03:42 | 3 | ||||||||||
|
BigWig and BigBed Resource Report Resource Website 10+ mentions |
BigWig and BigBed (RRID:SCR_007708) | BigWig and BigBed | software resource | Allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser. |
is listed by: OMICtools is related to: UCSC Genome Browser is related to: bedGraphToBigWig has parent organization: University of California at Santa Cruz; California; USA |
OMICS_00626 | SCR_007708 | 2026-08-01 12:03:40 | 32 | ||||||||||
|
HighSSR Resource Report Resource Website 1+ mentions |
HighSSR (RRID:SCR_007949) | HighSSR | software resource | Software that predicts microsatellites with Tandem Repeats Finder (TRF). |
is listed by: OMICtools has parent organization: Google Code |
PMID:22954626 | OMICS_00107 | SCR_007949 | highssr - Microsatellites prediction and analysis with next generation sequencing data | 2026-08-01 12:03:42 | 1 | ||||||||
|
GenoTan Resource Report Resource Website 1+ mentions |
GenoTan (RRID:SCR_007935) | GenoTan | software resource | A free software tool to identify length variation of microsatellites from short sequence reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24135263 | GNU General Public License, v3 | biotools:genotan | https://bio.tools/genotan | SCR_007935 | GenoTan - Genotyping of microsatellite loci | 2026-08-01 12:03:25 | 1 | |||||
|
RSEG Resource Report Resource Website 10+ mentions |
RSEG (RRID:SCR_007695) | RSEG | software resource | Software package aimed to analyze ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers, such as H3K36me3 and H3K27me3. |
is listed by: OMICtools has parent organization: University of Southern California; Los Angeles; USA |
PMID:21325299 | Free | OMICS_00459 | SCR_007695 | 2026-08-01 12:03:33 | 14 | ||||||||
|
HilbertVis Resource Report Resource Website 1+ mentions |
HilbertVis (RRID:SCR_007862) | HilbertVis | software resource | Software tool that allows to display very long data vectors in a space-efficient manner, allowing the user to visually judge the large scale structure and distribution of features simultaneously with the rough shape and intensity of individual features. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
DOI:10.1093/bioinformatics/btp152 | OMICS_00627, biotools:hilbertvis | https://bio.tools/hilbertvis, https://sources.debian.org/src/r-bioc-hilbertvis/ | SCR_007862 | 2026-08-01 12:03:34 | 4 | |||||||
|
BRIG Resource Report Resource Website 100+ mentions |
BRIG (RRID:SCR_007802) | BRIG | software resource | A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
DOI:10.1186/1471-2164-12-402 | OMICS_00929, biotools:brig | https://bio.tools/brig, https://sources.debian.org/src/brig/ | SCR_007802 | BLAST Ring Image Generator | 2026-08-01 12:03:24 | 497 | ||||||
|
Annotation-Modules Resource Report Resource Website |
Annotation-Modules (RRID:SCR_008025) | Annotation-Modules | software resource | A tool for finding significant combinations of multisource annotations in gene lists. | is listed by: OMICtools | OMICS_00630 | SCR_008025 | 2026-08-01 12:03:25 | 0 | ||||||||||
|
BiQAnalyzer HT Resource Report Resource Website 10+ mentions |
BiQAnalyzer HT (RRID:SCR_008045) | BiQAnalyzer HT | software resource | Software that currently allows to process an amount of bisulfite sequencing reads obtained in one or several bisulfite sequencing experiments. | is listed by: OMICtools | OMICS_00631 | SCR_008045 | 2026-08-01 12:03:26 | 12 | ||||||||||
|
lobSTR Resource Report Resource Website 10+ mentions |
lobSTR (RRID:SCR_008030) | lobSTR | software resource | A software tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data., 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: Massachusetts Institute of Technology; Massachusetts; USA; |
PMID:22522390 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00109, biotools:lobstr | https://bio.tools/lobstr | SCR_008030 | lobSTR - Profiling STRs in personal genomes | 2026-08-01 12:03:43 | 47 |
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