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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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shapeit4 Resource Report Resource Website 10+ mentions |
shapeit4 (RRID:SCR_024335) | software resource, software application | Software tool for estimation of haplotypes aka phasing for SNP array and high coverage sequencing data. The version 4 is refactored and improved version of SHAPEIT algorithm with multiple key additional features. | estimation of haplotypes, phasing, SNP array data, high coverage sequencing data, | is listed by: Debian | PMID:31780650 | Free, Available for download, Freely available, | https://sources.debian.org/src/shapeit4/ | SCR_024335 | SHAPEIT, SHAPEIT4 | 2026-08-01 12:11:23 | 21 | |||||||
|
CARD Resource Report Resource Website 100+ mentions |
CARD (RRID:SCR_023995) | data or information resource, database | Comprehensive antibiotic resistance database. Bioinformatic database of resistance genes, their products and associated phenotypes. | Antibiotic resistance data, resistance genes and associated phenotypes, resistance genes, phenotypes, | is listed by: Debian | PMID:31665441 | Free, Available for download, Freely available | r3d100012727 | https://doi.org/10.17616/R3WN59 | https://sources.debian.org/src/card-rgi/ | SCR_023995 | card-rgi, Comprehensive Antibiotic Resistance Database, The Comprehensive Antibiotic Resistance Database | 2026-08-01 12:11:17 | 211 | |||||
|
sailfish Resource Report Resource Website 1+ mentions |
sailfish (RRID:SCR_024326) | software resource, software application | Software tool that implements novel, alignment free algorithm for estimation of isoform abundances directly from set of reference sequences and RNA-seq reads. | estimation of isoform abundances, reference sequences, RNA-seq reads, | is listed by: Debian | PMID:24752080 | Free, Available for download, Freely available, | OMICS_03939 | https://sources.debian.org/src/sailfish/ | SCR_024326 | 2026-08-01 12:11:19 | 1 | |||||||
|
ragout Resource Report Resource Website 1+ mentions |
ragout (RRID:SCR_024206) | software resource, software application | 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 | 2026-08-01 12:11:23 | 1 | |||||||
|
Bio-SamTools Resource Report Resource Website 1+ mentions |
Bio-SamTools (RRID:SCR_024066) | software resource, software application | Software Perl interface to SamTools library for DNA sequencing. | Perl interface, SamTools library, DNA sequencing, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-samtools-perl/ | SCR_024066 | libbio-samtools-perl | 2026-08-01 12:11:22 | 5 | ||||||||
|
skesa Resource Report Resource Website 1+ mentions |
skesa (RRID:SCR_024341) | software resource, software application | 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 | 2026-08-01 12:11:22 | 8 | |||||||
|
sistr Resource Report Resource Website 10+ mentions |
sistr (RRID:SCR_024342) | SISTR | software resource, software application | 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 | 2026-08-01 12:11:20 | 21 | |||||
|
Bio-SCF Resource Report Resource Website |
Bio-SCF (RRID:SCR_024068) | software resource, software application | Software Perl extension for reading and writting SCF sequence files.This module provides Perl interface to SCF DNA sequencing files. It has both tied hash and an object-oriented interfaces. It provides the ability to read fields from SCF files and limited ability to modify them and write them back. | Perl, Perl extension, reading and writting SCF sequence files, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-scf-perl/ | SCR_024068 | Bio-SCF - Perl extension for reading and writting SCF sequence files, libbio-scf-perl | 2026-08-01 12:11:18 | 0 | ||||||||
|
pufferfish Resource Report Resource Website |
pufferfish (RRID:SCR_024184) | software resource, software application | Software tool implementing novel indexing data structure for compacted de Bruijn graph and colored compacted de Bruijn graph. | indexing data structure, compacted de Bruijn graph, colored compacted de Bruijn graph, | is listed by: Debian | PMID:29949982 | Free, Available for download, Freely available, | https://sources.debian.org/src/pufferfish/ | SCR_024184 | 2026-08-01 12:11:19 | 0 | ||||||||
|
rtax Resource Report Resource Website |
rtax (RRID:SCR_024320) | software resource, software application | 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 | 2026-08-01 12:11:19 | 0 | |||||||
|
runcircos-gui Resource Report Resource Website |
runcircos-gui (RRID:SCR_024321) | software resource, software application | 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 | 2026-08-01 12:11:19 | 0 | |||||||||
|
raccoon Resource Report Resource Website |
raccoon (RRID:SCR_024201) | software resource, software application | 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 | 2026-08-01 12:11:19 | 0 | |||||||
|
CamiTK Resource Report Resource Website |
CamiTK (RRID:SCR_023984) | software resource, software application | Software Computer Assisted Medical Intervention Tool Kit helps researchers and clinicians to easily and rapidly collaborate in order to prototype CAMI applications, that feature medical images, surgical navigation and biomechanical simulations.Open source, cross-platform generic tool, written in C++, which can handle medical images, surgical navigations and biomechanical simulations. | C++, medical images, surgical navigations, biomechanical simulations, | is listed by: Debian | DOI:10.1007/8415_2012_118 | Free, Available for download, Freely available | https://sources.debian.org/src/camitk/ | SCR_023984 | camitk, Computer Assisted Medical Intervention Tool Kit | 2026-08-01 12:11:17 | 0 | |||||||
|
roguenarok Resource Report Resource Website |
roguenarok (RRID:SCR_024316) | software resource, software application | 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 | 2026-08-01 12:11:19 | 0 | ||||||||
|
roadtrips Resource Report Resource Website |
roadtrips (RRID:SCR_024318) | software resource, software application | 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 | 2026-08-01 12:11:23 | 0 | ||||||
|
vcfanno Resource Report Resource Website |
vcfanno (RRID:SCR_024372) | software resource, software application | 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 | 2026-08-01 12:11:24 | 0 | |||||||
|
SeqLib Resource Report Resource Website 1+ mentions |
SeqLib (RRID:SCR_024091) | software resource, software application | 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 | libseqlib | 2026-08-01 12:11:18 | 1 | ||||||
|
VirulenceFinder Resource Report Resource Website 100+ mentions |
VirulenceFinder (RRID:SCR_024371) | software resource, software application | 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 | 2026-08-01 12:11:21 | 262 | ||||||
|
strap-base Resource Report Resource Website |
strap-base (RRID:SCR_024351) | software resource, software application | 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 | 2026-08-01 12:11:20 | 0 | |||||||||
|
qcat Resource Report Resource Website 10+ mentions |
qcat (RRID:SCR_024195) | software resource, software application | 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 | 2026-08-01 12:11:19 | 12 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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