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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-02-14 02:00:43 | 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 | 2026-02-14 02:01:00 | 6 | |||||||
|
VariationHunter Resource Report Resource Website 10+ mentions |
VariationHunter (RRID:SCR_004865) | VariationHunter | software resource | A software tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies. | structural variation, genome, next-generation sequencing |
is listed by: OMICtools is related to: SPLITREAD has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: SourceForge |
PMID:22048523 PMID:20529927 |
OMICS_00328 | SCR_004865 | VariationHunter-CommonLaw | 2026-02-14 02:00:46 | 12 | |||||||
|
Phymm and PhymmBL Resource Report Resource Website 10+ mentions |
Phymm and PhymmBL (RRID:SCR_004751) | Phymm, PhymmBL | software resource | Software for Phylogenetic Classification of Metagenomic Data with Interpolated Markov Models to taxonomically classify DNA sequences and accurately classify reads as short as 100 bp. PhymmBL, the hybrid classifier included in this distribution which combines analysis from both Phymm and BLAST, produces even higher accuracy. | metagenome, sequence, taxonomy, classification, phylogenetic classification, genome, short read |
is listed by: OMICtools has parent organization: University of Maryland; Maryland; USA |
NLM R01-LM006845 | PMID:19648916 PMID:21527926 |
Open-source license | OMICS_01461 | SCR_004751 | 2026-02-14 02:00:44 | 12 | ||||||
|
deStruct Resource Report Resource Website 1+ mentions |
deStruct (RRID:SCR_004747) | deStruct | software resource | A software tool for identifying structural variation in tumour genomes from whole genome illumina sequencing. | structural variation, genome, genomics |
is listed by: OMICtools has parent organization: Google Code |
Tumor, Cancer | Open unspecified license | OMICS_00314 | SCR_004747 | deStruct - Bioinformatics tool for identifying structural variation in tumour genomes | 2026-02-14 02:00:59 | 7 | ||||||
|
SLIQ Resource Report Resource Website 1+ mentions |
SLIQ (RRID:SCR_005003) | SLIQ | software resource | Software for simple linear inequalities based Mate-Pair reads filtering and scaffolding. A set of simple linear inequalities (SLIQ) derived from the geometry of contigs on the line that can be used to predict the relative positions and orientations of contigs from individual mate pair reads and thus produce a contig digraph. The SLIQ inequalities can also filter out unreliable mate pairs and can be used as a pre-processing step for any scaffolding algorithm. This tool filters mate pairs and then produces a Directed Contig Graph (contig diGraph). Also provided is a Naive scaffolder that can then produce scaffolds out of the contig diGraph. | python, scaffolding, contig position, contig orientation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Rutgers University; New Jersey; USA |
PMID:23057825 | biotools:sliq, OMICS_00048 | https://bio.tools/sliq | SCR_005003 | Simple linear inequalities, SLiQ: Simple linear inequalities based Mate-Pair reads filtering and scaffolding | 2026-02-14 02:01:03 | 3 | ||||||
|
cortex var Resource Report Resource Website 1+ mentions |
cortex var (RRID:SCR_005081) | cortex_var | software resource | A tool for genome assembly and variation analysis from sequence data. You can use it to discover and genotype variants on single or multiple haploid or diploid samples. If you have multiple samples, you can use Cortex to look specifically for variants that distinguish one set of samples (eg phenotype=X, cases, parents, tumour) from another set of samples (eg phenotype=Y, controls, child, normal). cortex_var features * Variant discovery by de novo assembly - no reference genome required * Supports multicoloured de Bruijn graphs - have multiple samples loaded into the same graph in different colours, and find variants that distinguish them. * Capable of calling SNPs, indels, inversions, complex variants, small haplotypes * Extremely accurate variant calling - see our paper for base-pair-resolution validation of entire alleles (rather than just breakpoints) of SNPs, indels and complex variants by comparison with fully sequenced (and finished) fosmids - a level of validation beyond that demanded of any other variant caller we are aware of - currently cortex_var is the most accurate variant caller for indels and complex variants. * Capable of aligning a reference genome to a graph and using that to call variants * Support for comparing cases/controls or phenotyped strains * Typical memory use: 1 high coverage human in under 80Gb of RAM, 1000 yeasts in under 64Gb RAM, 10 humans in under 256 Gb RAM | genome assembly, variation analysis, sequence, variation, genotype variant, haploid, diploid, snp, indel, inversion, variant, haplotype, de novo assembly, genotyping, variant-calling, population analysis, population assembly |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Wellcome Trust Centre for Human Genetics |
PMID:22231483 | GNU General Public License, v3, Acknowledgement requested | OMICS_00056 | SCR_005081 | cortex_var - for variant and population assembly | 2026-02-14 02:01:03 | 3 | ||||||
|
SOPRA Resource Report Resource Website 10+ mentions |
SOPRA (RRID:SCR_005035) | SOPRA | software resource | Software tool to exploit the mate pair/paired-end information for assembly of short reads from high throughput sequencing platforms, e.g. Illumina and SOLiD. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Rutgers University; New Jersey; USA |
PMID:20576136 | Acknowledgement requested | biotools:sopra, OMICS_00049 | https://bio.tools/sopra | SCR_005035 | SOPRA - Statistical Optimization of Paired Read Assembly, Statistical Optimization of Paired Read Assembly | 2026-02-14 02:00:48 | 20 | |||||
|
SSPACE Resource Report Resource Website 100+ mentions |
SSPACE (RRID:SCR_005056) | SSPACE | software resource | A stand-alone software program for scaffolding pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads. | scaffolding, contig, genome, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21149342 DOI:10.1093/bioinformatics/btq683 |
GNU General Public License, Registration required | biotools:sspace, OMICS_00050 | https://bio.tools/sspace https://sources.debian.org/src/sspace/ |
SCR_005056 | 2026-02-14 02:01:02 | 426 | ||||||
|
HPC-CLUST Resource Report Resource Website 1+ mentions |
HPC-CLUST (RRID:SCR_005052) | HPC-CLUST | software resource | A set of tools designed to cluster large numbers (>1 million) of pre-aligned nucleotide sequences. It performs the clustering of sequences using the Hierarchical Clustering Algorithm (HCA). There are currently three different cluster metrics implemented: single-linkage, complete-linkage, and average-linkage. In addition, there are currently four sequence distance functions implemented, these are: identity (gap-gap counting as match), nogap (gap-gap being ignored), nogap-single (like nogap, but consecutive gap-nogap''s count as a single mismatch), tamura (distance is calculated with the knowledge that transitions are more likely than transversions). One advantage that HCA has over other algorithms is that instead of producing only the clustering at a given threshold, it produces the set of merges occuring at each threshold. With this approach, the clusters can afterwards very quickly be reported for every arbitrary threshold with little extra computation. This approach also allows the plotting of the variation of number of clusters with clustering threshold without requiring the clustering to be run for each threshold independently. Another feature of the way HPC-CLUST is implemented is that the single-, complete-, and average-linkage clusterings can be computed in a single run with little overhead. | c++, mpi |
is listed by: OMICtools has parent organization: University of Zurich; Zurich; Switzerland |
PMID:24215029 | OMICS_01446 | SCR_005052 | 2026-02-14 02:00:48 | 5 | ||||||||
|
M-pick Resource Report Resource Website |
M-pick (RRID:SCR_004995) | M-pick | software resource | A modularity-based clustering software for Operational Taxonomic Unit (OTU) picking of 16S rRNA sequences. The algorithm does not require a predetermined cut-off level, and our simulation studies suggest that it is superior to existing methods that require specified distance or variance levels to define OTUs. | 16s rrna sequence, 16s rrna, rrna, sequence, binning |
is listed by: OMICtools has parent organization: University of Florida; Florida; USA |
OMICS_01447 | SCR_004995 | M-pick: a modularity-based clustering method for OTU picking | 2026-02-14 02:01:01 | 0 | ||||||||
|
ESPRIT-Tree Resource Report Resource Website 1+ mentions |
ESPRIT-Tree (RRID:SCR_005045) | ESPRIT-Tree | software resource | Software for hierarchical Clustering Analysis of Millions of 16S rRNA Pyrosequences in Quasi-linear Time. | clustering, 16s rrna, pyrosequence |
is listed by: OMICtools has parent organization: University of Florida; Florida; USA |
PMID:21596775 | OMICS_01445 | SCR_005045 | ESPRIT-Tree: Hierarchical Clustering Analysis of Millions of 16S rRNA Pyrosequences in Quasi-linear Time | 2026-02-14 02:01:03 | 9 | |||||||
|
Time-series RNA-seq Analysis Package Resource Report Resource Website 1+ mentions |
Time-series RNA-seq Analysis Package (RRID:SCR_002935) | TRAP | software resource | A comprehensive software package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis for time-series data in a single environment. | time-series, rna-seq, analysis |
is listed by: OMICtools has parent organization: Seoul National University; Seoul; South Korea |
PMID:24518221 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02590 | SCR_002935 | 2026-02-14 02:00:35 | 3 | |||||||
|
pBuild Resource Report Resource Website 1+ mentions |
pBuild (RRID:SCR_002929) | software resource | A software tool that can compare several search engines' results and combine them together. | mass spectrometry, proteomics |
is listed by: OMICtools has parent organization: Chinese Academy of Sciences; Beijing; China |
OMICS_02468 | SCR_002929 | 2026-02-14 02:00:20 | 8 | ||||||||||
|
aCGH.Spline Resource Report Resource Website |
aCGH.Spline (RRID:SCR_002927) | software resource | An R package for array comparative genomic hybridization (aCGH) dye bias normalization. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:21357574 | Free, Available for download, Freely available | OMICS_02607 | http://cran.r-project.org/web/packages/aCGH.Spline/ | SCR_002927 | 2026-02-14 02:00:28 | 0 | |||||||
|
StreamingTrim Resource Report Resource Website 1+ mentions |
StreamingTrim (RRID:SCR_002922) | software resource | A DNA reads trimming software, written in Java, with which researchers are able to analyse the quality of DNA sequences in fastq files and to search for low-quality zones in a very conservative way. | standalone software, java, 16s rrna, sequence | is listed by: OMICtools | PMID:24128146 | Free, Available for download, Freely available | OMICS_05196 | SCR_002922 | 2026-02-14 02:00:35 | 8 | ||||||||
|
pLabel Resource Report Resource Website 10+ mentions |
pLabel (RRID:SCR_002923) | software resource | Mass spectral peak labeling software developed for proteomics research., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | mass spectrometry, proteomics |
is listed by: OMICtools has parent organization: Chinese Academy of Sciences; Beijing; China |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02469 | SCR_002923 | 2026-02-14 02:00:20 | 28 | |||||||||
|
hot scan Resource Report Resource Website 1+ mentions |
hot scan (RRID:SCR_002840) | software resource | A free software to detect genomic regions unusually rich in translocation breakpoints. More generally, it may be used to detect a region that is unusually rich in a given character of a binary sequence. | software package, perl, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24860160 | Free, Freely available, Available for download | biotools:hot_scan, OMICS_05200 | https://bio.tools/hot_scan | SCR_002840 | hot_scan | 2026-02-14 02:00:33 | 6 | ||||||
|
rDock Resource Report Resource Website 100+ mentions |
rDock (RRID:SCR_002838) | software resource | A fast and versatile Open Source docking software program that can be used to dock small molecules against proteins and nucleic acids. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24722481 | Free, Freely available, Available for download | OMICS_03835 | SCR_002838 | 2026-02-14 02:00:27 | 113 | ||||||||
|
Basic4Cseq Resource Report Resource Website 1+ mentions |
Basic4Cseq (RRID:SCR_002836) | software resource | An R/Bioconductor package for basic filtering, analysis and subsequent near-cis visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile. | software package, unix/linux, mac os x, windows, r, quality control, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25078398 | Free, Freely available, Available for download | OMICS_05202 | SCR_002836 | Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data | 2026-02-14 02:00:19 | 6 |
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