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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Porechop Resource Report Resource Website 1000+ mentions |
Porechop (RRID:SCR_016967) | software resource, software application, data processing software | Software tool for finding and removing adapters from Oxford Nanopore reads. | finding, removing, adapter, Oxford Nanopore, read, sequencing, data |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_17306 | https://sources.debian.org/src/porechop/ | SCR_016967 | 2026-08-08 12:03:22 | 1350 | ||||||||
|
MEGAHIT Resource Report Resource Website 1000+ mentions |
MEGAHIT (RRID:SCR_018551) | software resource, software application, data processing software | Software tool as Next Generation Sequencing assembler. Optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single cell assembly. Can assemble genome sequences from metagenomic datasets of hundreds of Giga base-pairs in time and memory efficient manner on single server. | NGS metagenome, Next Generation Sequencing assembler, metagenome, genome assembly, genome sequence, metagenomic dataset, giga base pairs, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Hong Kong GRF ; Innovation and Technology Fund |
PMID:25609793 PMID:27012178 |
Free, Available for download, Freely available | OMICS_07234, biotools:megahit | https://bio.tools/megahit, https://sources.debian.org/src/megahit/ | SCR_018551 | MEGAHIT v0.1 | 2026-08-08 12:03:25 | 1897 | |||||
|
gffread Resource Report Resource Website 10+ mentions |
gffread (RRID:SCR_018965) | software resource, software application, data processing software | Open source software tool to manipulate files in GFF format. Used to convert, sort, filter, transform, or cluster genomic features. | Gene annotation, transcriptome analysis, GFF file format, convert, sort, filter, transform, cluster genomic feature |
is listed by: Debian is listed by: OMICtools |
DOI:10.12688/f1000research.23297.1 | Free, Available for download, Freely available | OMICS_28050 | https://github.com/gpertea/gffread, https://sources.debian.org/src/gffread/ | SCR_018965 | General Feature Format Read, GFF Read | 2026-08-08 12:03:21 | 45 | ||||||
|
mosdepth Resource Report Resource Website 50+ mentions |
mosdepth (RRID:SCR_018929) | software resource, software application, data processing software | Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes. | Calculating genome, wide sequencing coverage, depth measurement, BAM file, CRAM file, nucleotide position, genome, genomic region set, WGS exom, targeted sequencing, coverage calculation, exom, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG006693; NHGRI R01 HG009141; NIGMS R01 GM124355; NCI U24 CA209999 |
PMID:29096012 | Free, Available for download, Freely available | OMICS_20873, biotools:mosdepth | https://bio.tools/mosdepth, https://sources.debian.org/src/mosdepth/ | SCR_018929 | 2026-08-08 12:03:26 | 56 | ||||||
|
Vmatch Resource Report Resource Website 50+ mentions |
Vmatch (RRID:SCR_018968) | sequence analysis software, software resource, software application, data analysis software, data processing software | Software tool for efficiently solving large scale sequence matching tasks. | Sequence analysis, large scale, sequence matching, sequence, matching, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Hamburg; Hamburg; Germany |
Free, Available for download, Freely available | OMICS_19963, biotools:vmatch | https://bio.tools/vmatch, https://sources.debian.org/src/vmatch/ | SCR_018968 | 2026-08-08 12:01:25 | 56 | ||||||||
|
BRAKER Resource Report Resource Website 500+ mentions |
BRAKER (RRID:SCR_018964) | software resource, software application, simulation software | Software tool as pipeline for accurate and automated gene prediction in novel eukaryotic genomes. Automated gene prediction training and gene prediction pipeline.BRAKER1 is eukaryotic genome annotation pipeline. BRAKER2 is extension of BRAKER1 which allows for fully automated training of gene prediction tools GeneMark EX R14, R15, R17, F1 and AUGUSTUS from RNA Seq and/or protein homology information, and that integrates extrinsic evidence from RNA-Seq and protein homology information into prediction. | Automated gene prediction, novel eukaryotic genomes, gene prediction training, gene prediction pipeline, protein coding gene structure, gene structure prediction, eukaryotic genome, RNA-Seq, protein homology |
uses: Augustus is listed by: Debian is listed by: OMICtools |
NHGRI HG000783; German Research Foundation |
PMID:31020555 DOI:10.1101/2020.08.10.245134 |
Free, Available for download, Freely available | OMICS_10582 | https://sources.debian.org/src/braker/ | SCR_018964 | BRAKER2, BRAKER1 | 2026-08-08 12:01:22 | 531 | |||||
|
Seqtk Resource Report Resource Website 1000+ mentions |
Seqtk (RRID:SCR_018927) | sequence analysis software, software resource, software application, data analysis software, data processing software | Software fast and lightweight tool for processing sequences in FASTA or FASTQ format. | Sequence processing, FASTA format, FASTQ format, data processing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_09736, biotools:seqtk | https://bio.tools/seqtk, https://sources.debian.org/src/seqtk/ | SCR_018927 | SEQTK | 2026-08-08 12:01:21 | 1039 | |||||||
|
CAZy- Carbohydrate Active Enzyme Resource Report Resource Website 1000+ mentions |
CAZy- Carbohydrate Active Enzyme (RRID:SCR_012909) | CAZy | database, data or information resource | Database that describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. This specialist database is dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description. An original aspect of the CAZy database is its attempt to cover all carbohydrate-active enzymes across organisms and across subfields of glycosciences. One can search for CAZY Family pages using the Protein Accession (Genpept Accession, Uniprot Accession or PDB ID), Cazy family name or EC number. In addition, genomes can be searched using the NCBI TaxID. This search can be complemented by Google-based searches on the CAZy site. | carbohydrate, carbohydrate-binding, carbohydrate binding module, carbohydrate esterase, catalytic binding, glycosidic bond, glycosidic hydrolase, glycosyl transferase, polysaccharide lyase, enzyme class, enzyme, module, genome, virus, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: OMICtools has parent organization: Aix-Marseille University; Provence-Alpes-Cote d'Azur; France |
PMID:24270786 | r3d100012321, biotools:cazy, OMICS_01677, nif-0000-02642, SCR_012935 | https://bio.tools/cazy | SCR_012909 | Carbohydrate-Active enZYme, Carbohydrate-Active enZYmes Database | 2026-08-08 12:02:43 | 2435 | ||||||
|
SOAPsnp Resource Report Resource Website 100+ mentions |
SOAPsnp (RRID:SCR_010602) | SOAPsnp | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software providng a method based on Bayes? theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors., 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 |
DOI:10.1101/gr.088013.108 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:soapsnp, OMICS_00078 | https://bio.tools/soapsnp, https://sources.debian.org/src/soapsnp/ | SCR_010602 | 2026-08-08 11:59:33 | 207 | ||||||
|
TargetMiner Resource Report Resource Website 50+ mentions |
TargetMiner (RRID:SCR_010573) | TargetMiner | production service resource, software resource, data analysis service, analysis service resource, service resource | A robust tool for microRNA target prediction with systematic identification of negative examples. | is listed by: OMICtools | Free for academic use | OMICS_00419 | SCR_010573 | 2026-08-08 11:59:22 | 89 | |||||||||
|
JR-Assembler Resource Report Resource Website 1+ mentions |
JR-Assembler (RRID:SCR_010681) | JR-Assembler | software resource | An assembler for the de novo assembly of large genomes using short sequence reads via jumping extension and read remapping. | is listed by: OMICtools | PMID:23966565 | OMICS_00018 | SCR_010681 | 2026-08-08 11:59:34 | 4 | |||||||||
|
EULER-SR Resource Report Resource Website 10+ mentions |
EULER-SR (RRID:SCR_010485) | EULER-SR | software resource | Assembly package that contains a suite of software programs for correcting errors in short reads and assembling them. The assembler may take as input classical Sanger reads, 454 sequences, and Illumina reads. | fragment assembly, short read, read |
is listed by: OMICtools is listed by: Debian has parent organization: University of California at San Diego; California; USA |
PMID:18083777 DOI:10.1101/gr.7088808 |
OMICS_00015 | http://ngslib.i-med.ac.at/node/64, https://sources.debian.org/src/euler-sr/ | SCR_010485 | EULER: short reads assembler | 2026-08-08 11:59:32 | 17 | ||||||
|
MicroMUMMIE Resource Report Resource Website 1+ mentions |
MicroMUMMIE (RRID:SCR_010847) | MicroMUMMIE | software resource | Software for a specific model, implemented within the MUMMIE framework, for predicting micro-RNA binding sites using PAR-CLIP data. |
is listed by: OMICtools has parent organization: Duke University; North Carolina; USA |
PMID:23708386 | OMICS_00401 | SCR_010847 | 2026-08-08 11:59:37 | 1 | |||||||||
|
miRDB Resource Report Resource Website 1000+ mentions |
miRDB (RRID:SCR_010848) | miRDB | data or information resource, production service resource, data analysis service, database, analysis service resource, service resource | An online database for miRNA target prediction and functional annotations. | mirna, target, pathway, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:18426918 PMID:18048393 |
OMICS_00403, biotools:miRDb | https://bio.tools/miRDB | SCR_010848 | 2026-08-08 11:59:24 | 2027 | |||||||
|
SICER Resource Report Resource Website 100+ mentions |
SICER (RRID:SCR_010843) | SICER | software resource | A clustering software package for identification of enriched domains from histone modification ChIP-Seq data. | python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: George Washington University; Washington D.C.; USA |
PMID:19505939 | biotools:sicer, OMICS_00461 | https://bio.tools/sicer | SCR_010843 | SICER: A clustering approach for identification of enriched domains from histone modification ChIP-Seq data | 2026-08-08 11:59:37 | 420 | ||||||
|
MapSplice Resource Report Resource Website 100+ mentions |
MapSplice (RRID:SCR_010844) | MapSplice | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Accurate mapping of RNA-seq reads for splice junction discovery. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Kentucky; Kentucky; USA |
PMID:20802226 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mapsplice, OMICS_01243 | https://bio.tools/mapsplice | SCR_010844 | 2026-08-08 11:59:24 | 214 | ||||||
|
TargetScan Resource Report Resource Website 10000+ mentions |
TargetScan (RRID:SCR_010845) | production service resource, web service, software resource, data access protocol, data analysis service, analysis service resource, service resource | Web tool to predict biological targets of miRNAs by searching for presence of conserved 8mer, 7mer and 6mer sites that match seed region of each miRNA. Nonconserved sites are also predicted and sites with mismatches in seed region that are compensated by conserved 3' pairing. Used to search for predicted microRNA targets in mammals. | predict, biological, target, miRNA, conserved, 8mer, 7mer, site, match seed, region, nonconserved, mismatched, pair |
is listed by: OMICtools is listed by: SoftCite has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
NIGMS GM067031; Howard Hughes Medical Institute ; NSF Graduate Research Fellowship |
PMID:26267216 | Free, Freely available | OMICS_00420 | http://www.targetscan.org/vert_71/ | SCR_010845 | TargetScanFly | 2026-08-08 11:59:38 | 11785 | |||||
|
miRNAminer Resource Report Resource Website 1+ mentions |
miRNAminer (RRID:SCR_010850) | miRNAminer | production service resource, software resource, data analysis service, analysis service resource, service resource | A web-based tool used for homologous miRNA gene search in several species. The code is available on request. |
is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
PMID:18215311 | Acknowledgement requested | OMICS_00409 | SCR_010850 | 2026-08-08 11:59:38 | 2 | ||||||||
|
MIRA Resource Report Resource Website 1000+ mentions |
MIRA (RRID:SCR_010731) | MIRA | software resource | Sequence assembler and mapper for whole genome shotgun and EST/RNASeq sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge is required by: MITObim |
PMID:15140833 DOI:10.1101/gr.1917404 |
OMICS_00023, biotools:mira | https://bio.tools/mira | https://sources.debian.org/src/mira-assembler/ | SCR_010731 | Mimicking Intelligent Read Assembly | 2026-08-08 11:59:23 | 1047 | |||||
|
PE-Assembler Resource Report Resource Website 1+ mentions |
PE-Assembler (RRID:SCR_010732) | PE-Assembler | software resource | Software providing a method that eschews the traditional graph-based approach in favor of a simple 3'' extension approach that has potential to be massively parallelized. | is listed by: OMICtools | OMICS_00025 | SCR_010732 | 2026-08-08 11:59:34 | 3 |
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