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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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vcfanno Resource Report Resource Website 1+ mentions |
vcfanno (RRID:SCR_024372) | software application, software resource | Software tool for flexible annotation of genetic variants.Extracts and summarizes attributes from multiple annotation files and integrates annotations within INFO column of the original VCF file. | annotation of genetic variants, extracts and summarizes attributes, multiple annotation files, integrates annotations, VCF file, | is listed by: Debian | PMID:27250555 | Free, Available for download, Freely available, | OMICS_11863 | https://sources.debian.org/src/vcfanno/ | SCR_024372 | SciCrunch Registry | 2026-10-24 12:52:00 | 1 | |||||||
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SeqLib Resource Report Resource Website 1+ mentions |
SeqLib (RRID:SCR_024091) | software application, software resource | Software C++ htslib/bwa-mem/fermi interface for interrogating sequence data | interrogating sequence data, | is listed by: Debian | DOI:10.1093/bioinformatics/btw741 | Free, Available for download, Freely available, | OMICS_14682 | https://sources.debian.org/src/libseqlib/ | SCR_024091 | SciCrunch Registry | libseqlib | 2026-10-24 12:51:59 | 1 | ||||||
|
VirulenceFinder Resource Report Resource Website 100+ mentions |
VirulenceFinder (RRID:SCR_024371) | software application, software resource | Software tool for detection of E. coli virulence genes. Used to identify viruelnce genes in total or partial sequenced isolates of bacteria. E. coli, Enterococcus, S. aureus and Listeria are available.for detection of E. coli virulence genes. | detection of E. coli virulence genes, | is listed by: Debian | PMID:24574290 | Free, Available for download, Freely available, | OMICS_17862 | https://sources.debian.org/src/virulencefinder/ | SCR_024371 | SciCrunch Registry | virulencefinder | 2026-10-24 12:52:00 | 301 | ||||||
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strap-base Resource Report Resource Website 1+ mentions |
strap-base (RRID:SCR_024351) | software application, software resource | Software tool as Intuitive Editor for annotated multiple Sequence and Structure Alignments. | editor for annotated multiple Sequence and Structure Alignments, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/strap-base/ | SCR_024351 | SciCrunch Registry | 2026-10-24 12:52:00 | 3 | |||||||||
|
qcat Resource Report Resource Website 10+ mentions |
qcat (RRID:SCR_024195) | software application, software resource | Software Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files. | command-line tool, demultiplexing Oxford Nanopore reads, reads from FASTQ files, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/qcat/ | SCR_024195 | SciCrunch Registry | 2026-10-24 12:51:59 | 22 | |||||||||
|
MacSyFinder Resource Report Resource Website 10+ mentions |
MacSyFinder (RRID:SCR_024106) | software application, software resource | Software tool to mine genomes for molecular systems with Application to CRISPR-Cas Systems. Detection of macromolecular systems in protein datasets using systems modelling and similarity search. | Detection of macromolecular system, protein datasets, mine genomes, molecular systems, | is listed by: Debian | PMID:25330359 | Free, Available for download, Freely available, | OMICS_20116 | https://sources.debian.org/src/macsyfinder/ | SCR_024106 | SciCrunch Registry | macsyfinder | 2026-10-24 12:51:59 | 28 | ||||||
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tiddit Resource Report Resource Website 1+ mentions |
tiddit (RRID:SCR_024361) | software application, software resource | Software tool as structural variant calling. | structural variant calling, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/tiddit/ | SCR_024361 | SciCrunch Registry | TIDDIT | 2026-10-24 12:52:00 | 3 | ||||||||
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Yanagiba Resource Report Resource Website |
Yanagiba (RRID:SCR_024362) | software application, software resource | Software tool to filter and slice Nanopore reads which have been basecalled with Albacore. | filter and slice Nanopore reads, basecalled with Albacore, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/yanagiba/ | SCR_024362 | SciCrunch Registry | yanagiba | 2026-10-24 12:52:00 | 0 | ||||||||
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Nanocall Resource Report Resource Website |
Nanocall (RRID:SCR_024124) | software application, software resource | Software basecaller for Oxford Nanopore Technologies sequencing data. Oxford Nanopore Basecaller. | basecaller, Oxford Nanopore Technologies, sequencing data, | is listed by: Debian | PMID:27614348 | Free, Available for download, Freely available, | OMICS_11495 | https://sources.debian.org/src/nanocall/ | SCR_024124 | SciCrunch Registry | Nanocall, nanocall | 2026-10-24 12:51:59 | 0 | ||||||
|
swarm Resource Report Resource Website 1+ mentions |
swarm (RRID:SCR_024358) | software application, software resource | Software tool as clustering method for amplicon-based studies. | clustering method, amplicon based studies, | is listed by: Debian | PMID:26713226 | Free, Available for download, Freely available, | OMICS_14578 | https://sources.debian.org/src/swarm/ | SCR_024358 | SciCrunch Registry | 2026-10-24 12:52:00 | 5 | |||||||
|
OmicsOffice for NGS SeqSolve Resource Report Resource Website |
OmicsOffice for NGS SeqSolve (RRID:SCR_001222) | OmicsOffice for NGS | commercial organization, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software for secondary and tertiary analysis of Next Generation Sequencing (NGS) data. | next-generation sequencing, rna-seq, chip-seq, transcript, alternative splicing, variant, mirna, non-coding rna expression, genome, differential expression, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20671709 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:seqsolve, OMICS_02111 | https://bio.tools/seqsolve | SCR_001222 | SciCrunch Registry | OmicsOffice for NGS (SeqSolve), SeqSolve | 2026-10-24 12:52:03 | 0 | |||||
|
ZOOM Resource Report Resource Website 100+ mentions |
ZOOM (RRID:SCR_002175) | ZOOM | commercial organization, software resource | Software to map the Illumina/Solexa reads of 15x coverage of a human genome to the reference human genome in one CPU-day, allowing two mismatches, at full sensitivity. | next-generation sequencing, illumina, solexa, reference genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:18684737 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01852, biotools:zoom | https://bio.tools/zoom | SCR_002175 | SciCrunch Registry | ZOOM: Next Gen Sequencing | 2026-10-24 12:52:05 | 278 | |||||
|
Segway - a way to segment the genome Resource Report Resource Website 10+ mentions |
Segway - a way to segment the genome (RRID:SCR_004206) | software resource, source code | The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. The method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. Segway uses the Graphical Models Toolkit (GMTK) for efficient DBN inference. The software has extensive documentation and was designed from the outset with external users in mind. | genome annotation, source code, bayesian network model, bayesian, chip seq, dbn, bio.tools |
is used by: ENCODE is listed by: Debian is listed by: bio.tools has parent organization: University of Washington; Seattle; USA has parent organization: University of Toronto; Ontario; Canada |
PMID:22426492 | Free | biotools:segway, nlx_22911 | https://www.pmgenomics.ca/hoffmanlab/proj/segway/, https://bitbucket.org/hoffmanlab/segway/, https://bio.tools/segway | http://noble.gs.washington.edu/proj/segway/ | SCR_004206 | SciCrunch Registry | Segway | 2026-10-24 12:52:08 | 10 | |||||
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covtobed Resource Report Resource Website 1+ mentions |
covtobed (RRID:SCR_023998) | softwre application | Software tool to generate BED coverage tracks from BAM files. | generate BED coverage tracks, BAM files, | is listed by: Debian | DOI:10.21105/joss.02119 | Free, Available for download, Freely available | https://sources.debian.org/src/covtobed/ | SCR_023998 | SciCrunch Registry | 2026-10-24 12:49:37 | 1 | ||||||||
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GramAlign Resource Report Resource Website 1+ mentions |
GramAlign (RRID:SCR_024032) | alignment software, data processing software, image analysis software, software application, software resource | Software tool as time efficient progressive Multiple Sequence Alignment algorithm. Sequence distance estimation step is determined by the natural grammar present in nucleotide and amino acid sequences. | Multiple Sequence Alignment, progressive Multiple Sequence Alignment, sequence distance estimation, nucleotide and amino acid sequences, | is listed by: Debian | Free, Freely available | OMICS_05314 | https://sources.debian.org/src/gramalign/ | SCR_024032 | SciCrunch Registry | gramalign | 2026-10-24 12:49:38 | 4 | |||||||
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IDeFIX Resource Report Resource Website |
IDeFIX (RRID:SCR_024033) | data analysis software, data processing software, software application, software resource | Software tool for demultiplexing Illumina NGS data. Reports inconsistencies between the raw data and the Sample Sheet, checks for duplicates of indices/ index combinations in the latter and removes unwanted characters from it. Creates an IDeFIX_Report.csv containing the indices/ index combinations from the raw data and their abundance as well as their count in the Sample Sheet and the corresponding Index ID(s). | demultiplexing Illumina NGS data, reports inconsistencies, checks for duplicates of indices, removes unwanted characters, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/idefix/ | SCR_024033 | SciCrunch Registry | idefix | 2026-10-24 12:49:38 | 0 | ||||||||
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GraphMap2 Resource Report Resource Website 10+ mentions |
GraphMap2 (RRID:SCR_024035) | data analysis software, data processing software, software application, software resource | Software tool as splice aware RNA-seq mapper for long reads produced by Pacific Biosciences and Oxford Nanopore devices | splice aware RNA-seq mapper, long reads, Pacific Biosciences, Oxford Nanopore, | is listed by: Debian | PMID:27079541 | Free, Available for download, Freely available, | https://sources.debian.org/src/graphmap2/ | SCR_024035 | SciCrunch Registry | graphmap2 | 2026-10-24 12:49:37 | 21 | |||||||
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BioMAJ Resource Report Resource Website |
BioMAJ (RRID:SCR_023983) | data processing software, software application, software resource, workflow software | Software workflow engine dedicated to data synchronization and processing. Software automates the update cycle and the supervision of the locally mirrored databank repository. | workflow engine, data synchronization and processing, | is listed by: Debian | Free, Available for download, Freely available | OMICS_21717 | https://sources.debian.org/src/biomaj3/, http://genouest.github.io/biomaj/ | SCR_023983 | SciCrunch Registry | BioMAJ3, BIOlogie Mise A Jour, biomaj3 | 2026-10-24 12:49:37 | 0 | |||||||
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GNUmed Resource Report Resource Website |
GNUmed (RRID:SCR_024029) | software resource | Software to build Electronic Medical Record in multiple languages to assist and improve longitudinal care specifically in ambulatory settings.Useful to anyone documenting the health of patients including,doctors, physical therapists, occupational therapists,acupuncturists, nurses, psychologists. | build Electronic Medical Record, multiple languages | is listed by: Debian | Free, Freely available | https://sources.debian.org/src/gnumed-client/ | SCR_024029 | SciCrunch Registry | gnumed-client, gnumed-server, gnumed | 2026-10-24 12:49:37 | 0 | ||||||||
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Chemtool Resource Report Resource Website |
Chemtool (RRID:SCR_023992) | softwre application | Software tool for drawing organic molecules. Runs under the X Window System using the GTK widget set. Used for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11. | drawing organic molecules, drawing chemical structures, | is listed by: Debian | DOI:10.1002/nadc.20010491112 | Free, Available for download, Freely available | https://sources.debian.org/src/chemtool/ | SCR_023992 | SciCrunch Registry | chemtool | 2026-10-24 12:49:37 | 0 |
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