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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ragout Resource Report Resource Website 1+ mentions |
ragout (RRID:SCR_024206) | software application, software resource | Software tool for chromosome level scaffolding using multiple references. Given initial assembly fragments and one or multiple related references it produces chromosome scale assembly. | chromosome level scaffolding, multiple references, produce chromosome scale assembly, | is listed by: Debian | PMID:30341161 | Free, Available for download, Freely available, | OMICS_07883 | SCR_024206 | Reference-Assisted Genome Ordering UTility | 2026-08-04 09:45:28 | 1 | |||||||
|
skesa Resource Report Resource Website 1+ mentions |
skesa (RRID:SCR_024341) | software application, software resource | Software de-novo sequence read assembler for microbial genomes.Designed to create breaks at repeat regions in the genome. This leads to excellent sequence quality without significantly compromising contiguity.SKESA contigs could be connected into GFA graph using GFA connector. | de-novo sequence read assembler, microbial genomes, create breaks at repeat regions in genome, | is listed by: Debian | PMID:30286803 | Free, Available for download, Freely available, | https://sources.debian.org/src/skesa/ | SCR_024341 | SKESA | 2026-08-04 09:45:30 | 8 | |||||||
|
sistr Resource Report Resource Website 10+ mentions |
sistr (RRID:SCR_024342) | SISTR | software application, software resource | SISTR command-line tool. Open web accessible tool for rapidly typing and subtyping draft salmonella genome assemblies. | rapidly typing and subtyping draft salmonella genome assemblies, salmonella genome assemblies, | is listed by: Debian | PMID:26800248 | Free, Available for download, Freely available, | OMICS_12011 | https://sources.debian.org/src/sistr/ | SCR_024342 | Salmonella In Silico Typing Resource | 2026-08-04 09:45:30 | 21 | |||||
|
rtax Resource Report Resource Website |
rtax (RRID:SCR_024320) | software application, software resource | Software tool for rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene. | taxonomic classification, short paired-end sequence reads, 16S ribosomal RNA gene, | is listed by: Debian | PMID:22237546 | Free, Available for download, Freely available, | OMICS_28979 | https://sources.debian.org/src/rtax/ | SCR_024320 | 2026-08-04 09:45:29 | 0 | |||||||
|
runcircos-gui Resource Report Resource Website |
runcircos-gui (RRID:SCR_024321) | software application, software resource | GUI tool to run circos | run circos, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/runcircos-gui/ | SCR_024321 | 2026-08-04 09:45:30 | 0 | |||||||||
|
raccoon Resource Report Resource Website |
raccoon (RRID:SCR_024201) | software application, software resource | Software graphical interface for preparing AutoDock virtual screenings.Automates some of the most common operations performed when preparing virtual screening. | preparing AutoDock virtual screenings, automates operations for preparing virtual screening, | is listed by: Debian | PMID:21532931 | Free, Available for download, Freely available, | OMICS_21300 | https://sources.debian.org/src/raccoon/ | SCR_024201 | 2026-08-04 09:45:28 | 0 | |||||||
|
roguenarok Resource Report Resource Website |
roguenarok (RRID:SCR_024316) | software application, software resource | Software tool as versatile and scalable algorithm for rogue taxon identification. Also includes implementations of the maximum agreement subtree, leaf stability index and taxonomic instability index. | rogue taxon identification algorithm, maximum agreement subtree, leaf stability index, taxonomic instability index, | is listed by: Debian | PMID:22962004 | Free, Available for download, Freely available, | https://sources.debian.org/src/roguenarok/ | SCR_024316 | 2026-08-04 09:45:29 | 0 | ||||||||
|
roadtrips Resource Report Resource Website |
roadtrips (RRID:SCR_024318) | software application, software resource | Software C program that performs single SNP, case control association testing in samples with partially or completely unknown population and pedigree structure. | single SNP, case control association testing, testing samples, partially or completely unknown population, pedigree structure, | is listed by: Debian | PMID:20137780 | Free, Available for download, Freely available, | OMICS_21698 | https://sources.debian.org/src/roadtrips/ | SCR_024318 | ROADTRIPS 2.0 | 2026-08-04 09:45:30 | 0 | ||||||
|
vcfanno Resource Report Resource Website |
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 | 2026-08-04 09:45:30 | 0 | |||||||
|
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 | virulencefinder | 2026-08-04 09:45:31 | 262 | ||||||
|
strap-base Resource Report Resource Website |
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 | 2026-08-04 09:45:30 | 0 | |||||||||
|
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 | 2026-08-04 09:45:28 | 12 | |||||||||
|
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 | TIDDIT | 2026-08-04 09:45:30 | 3 | ||||||||
|
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 | yanagiba | 2026-08-04 09:45:30 | 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 | 2026-08-04 09:45:30 | 4 | |||||||
|
PhenoFam Resource Report Resource Website |
PhenoFam (RRID:SCR_000640) | PhenoFam | software application, software resource | A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms. | java, javascript, gene, gene set enrichment analysis, structure, function, protein domain, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20478033 | Free, Available for download, Freely available | OMICS_02230, biotools:phenofam | https://bio.tools/phenofam | SCR_000640 | 2026-08-04 09:40:11 | 0 | ||||||
|
FLOSS Resource Report Resource Website |
FLOSS (RRID:SCR_000836) | FLOSS | software application, software resource | Software application that performs ordered subset analysis using MERLIN's ouput .lod file created with the --perFamily option. Ordered subset analysis uses covariate information to identify a more homogenous subset of families for linkage analysis. The homogeneous subset of families does not need to be specified a priori, and the covariates can include environmental exposures, quantitative traits, or linkage scores at another locus in the genome. The evidence for linkage is evaluated with a permutation test. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:floss, nlx_154319 | https://bio.tools/floss | SCR_000836 | FLexible Ordered SubSet analysis | 2026-08-04 09:40:14 | 0 | |||||||
|
DINDEL Resource Report Resource Website 10+ mentions |
DINDEL (RRID:SCR_001827) | Dindel | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software program for calling small indels from short-read sequence data ("next generation sequence data"). It is currently designed to handle only Illumina data. Dindel takes BAM files with mapped Illumina read data and enables researchers to detect small indels and produce a VCF file of all the variant calls. It has been written in C++ and can be used on Linux-based and Mac computers (it has not been tested on Windows operating systems). | indel, short-read, next generation sequence, illumina, gene, genetic, genomic, c++, linux, macos, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:20980555 DOI:10.1101/gr.112326.110 |
THIS RESOURCE IS NO LONGER IN SERVICE | , nlx_154283, OMICS_00096, biotools:dindel | https://bio.tools/dindel, https://sources.debian.org/src/dindel/ | http://www.sanger.ac.uk/resources/software/dindel/ | SCR_001827 | Dindel: Accurate indel calls from short-read data | 2026-08-04 09:40:29 | 44 | ||||
|
PEDIGRAPH Resource Report Resource Website 10+ mentions |
PEDIGRAPH (RRID:SCR_001938) | Pedigraph | software application, software resource | A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles | gene, genetic, genomic, c, c++, ms-windows, linux, pedigree, java, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
PMID:14986440 | Acknowledgement required, Copyrighted | biotools:pedigraph, OMICS_00212, nlx_154519 | https://bio.tools/pedigraph | SCR_001938 | 2026-08-04 09:40:30 | 17 | ||||||
|
Apollo Resource Report Resource Website 100+ mentions |
Apollo (RRID:SCR_001936) | Apollo | software application, software resource | A standalone Java application with a GUI (graphical user interface) for editing genome annotations. Like GBrowse, it allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off GFF3 or a Chado database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses. | java, genome annotation, genome, annotation, windows, mac os x, linux, solaris, unix, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Generic Model Organism Database Project |
PMID:19439563 PMID:12537571 DOI:10.1186/gb-2002-3-12-research0082 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11761, biotools:apollo, OMICS_01933 | https://bio.tools/apollo, https://sources.debian.org/src/aragorn/ | SCR_001936 | 2026-08-04 09:40:30 | 274 |
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