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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ABACAS Resource Report Resource Website 100+ mentions |
ABACAS (RRID:SCR_015852) | ABACAS | software application, software resource | Software that contiguates (align, order, orientate), visualizes and designs primers to close gaps on shotgun assembled contigs based on a reference sequence. ABACAS finds alignment positions and identifies syntenies of assembled contigs against the reference, then generates a pseudomolecule taking overlapping contigs and gaps into account. | contiguation, primer, shotgun assembled contig, reference sequence, assembled sequence |
is listed by: Debian is listed by: OMICtools |
European Union LSHP-LT-2004-503578; Wellcome Trust Sanger Institute |
Free, Available for download | OMICS_06933 | https://sourceforge.net/projects/abacas/files/, https://sources.debian.org/src/abacas/ | SCR_015852 | ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences, Algorithm Based Automatic Contiguation of Assembled Sequences (ABACAS), Algorithm Based Automatic Contiguation of Assembled Sequences | 2026-07-26 09:06:26 | 174 | |||||
|
DOMAINATRIX Resource Report Resource Website |
DOMAINATRIX (RRID:SCR_016084) | software application, software resource | Software for protein domain search. It is a part of Embassy software package. | protein, domain, search, molecular, biology | is listed by: Debian | Free, Available for download, Freely available | http://emboss.sourceforge.net/what/, https://sources.debian.org/src/embassy-domainatrix/ | SCR_016084 | Embassy-domainatrix | 2026-07-26 09:06:40 | 0 | ||||||||
|
Ecopcr Resource Report Resource Website 10+ mentions |
Ecopcr (RRID:SCR_016082) | Ecopcr | software application, software resource | Software for Electronic PCR that estimates PCR barcode primers quality and develops new barcode primers. In conjunction with OBITools, users can postprocess ecoPCR output to compute barcode coverage and barcode specificity., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | electronic, PCR, estimate, primers, quality, barcode |
is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_19861 | https://sources.debian.org/src/ecopcr/ | http://www.grenoble.prabi.fr/trac/ecoPCR/ | SCR_016082 | Ecopcr: Electronic polymerase chain reaction | 2026-07-26 09:06:33 | 27 | |||||
|
QGIS Resource Report Resource Website 100+ mentions |
QGIS (RRID:SCR_018507) | software application, software resource | Open source cross platform desktop geographic information system application that supports viewing, editing, and analysis of geospatial data. Functions as geographic information system software, allowing users to analyze and edit spatial information, in addition to composing and exporting graphical maps. | Geographic information system, viewing, editing, analysis, geospatial data, spatial information analysis, graphical map, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:QGIS | https://bio.tools/QGIS | SCR_018507 | 2026-07-26 09:07:14 | 400 | ||||||||
|
Clinotator Resource Report Resource Website 1+ mentions |
Clinotator (RRID:SCR_016054) | software application, software resource | Software that performs clinical interpretation of ambiguous ClinVar annotations. This software takes batches of variants as input and queries NCBI eutilities to generate scoring metrics. | clinical, age, weight, score, metric, vcf, python, nbci, annotation, variant, scoring, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free | biotools:clinotator | https://bio.tools/clinotator | SCR_016054 | clinotator.py | 2026-07-26 09:06:31 | 2 | |||||||
|
Bio-ASN1-EntrezGene Resource Report Resource Website |
Bio-ASN1-EntrezGene (RRID:SCR_024056) | software application, software resource | Software regular expression based Perl Parser for NCBI Entrez Gene genome databases. Parses ASN.1-formatted Entrez Gene record and returns data structure that contains all data items from gene record. | Perl parser, NCBI Entrez Gene genome databases parser, ASN.1-formatted Entrez Gene record parser, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-asn1-entrezgene-perl/ | SCR_024056 | libbio-asn1-entrezgene-perl, Bio-ASN1-EntrezGene - Regular expression-based Perl Parser for NCBI Entrez Gene | 2026-07-26 09:08:18 | 0 | ||||||||
|
AcePerl Resource Report Resource Website |
AcePerl (RRID:SCR_024057) | software application, software resource | Software provides an interface to the ACEDB object-oriented database. Both read and write access is provided, and ACE objects are returned as similarly-structured Perl objects. Multiple databases can be opened simultaneously. | software interface, provides interface to ACEDB object-oriented database, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libace-perl/, https://github.com/WormBase/AcePerl | SCR_024057 | Ace, ACE, libace-perl, Ace-Perl, ace-perl, Ace - Object-Oriented Access to ACEDB Databases | 2026-07-26 09:08:18 | 0 | ||||||||
|
shapeit4 Resource Report Resource Website 10+ mentions |
shapeit4 (RRID:SCR_024335) | software application, software resource | 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 | 2026-07-26 09:08:24 | 21 | |||||||
|
sailfish Resource Report Resource Website 1+ mentions |
sailfish (RRID:SCR_024326) | software application, software resource | 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 | 2026-07-26 09:08:24 | 1 | |||||||
|
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 | 2026-07-26 09:08:19 | 1 | |||||||
|
Bio-SamTools Resource Report Resource Website 1+ mentions |
Bio-SamTools (RRID:SCR_024066) | software application, software resource | 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 | 2026-07-26 09:08:16 | 5 | ||||||||
|
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 | 2026-07-26 09:08:25 | 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 | 2026-07-26 09:08:24 | 21 | |||||
|
Bio-SCF Resource Report Resource Website |
Bio-SCF (RRID:SCR_024068) | software application, software resource | 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 | 2026-07-26 09:08:19 | 0 | ||||||||
|
pufferfish Resource Report Resource Website |
pufferfish (RRID:SCR_024184) | software application, software resource | 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 | 2026-07-26 09:08:23 | 0 | ||||||||
|
BioCocoa Resource Report Resource Website |
BioCocoa (RRID:SCR_023977) | software application, software resource | Open source framework for bioinformatics written in Objective-C. Provides Cocoa and GNUstep programmers with full suite of APIs for handling and manipulating biological sequences. | APIs for handling and manipulating biological sequences, | is listed by: Debian | Free, Available for download, Freely available | OMICS_19790 | https://sources.debian.org/src/biococoa/ | SCR_023977 | biococoa | 2026-07-26 09:08:15 | 0 | |||||||
|
Biber Resource Report Resource Website |
Biber (RRID:SCR_023973) | software application, software resource | Software bibliography processing backend for LaTeX biblatex package. Supports unsurpassed feature set for automated conformance to complex bibliography style requirements such as labelling, sorting and name handling. BibTeX replacement for users of BibLaTeX. | bibliography processing backend, LaTeX biblatex package, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/biber/, https://sourceforge.net/projects/biblatex-biber/files/latest/download | SCR_023973 | biber | 2026-07-26 09:08:16 | 0 | ||||||||
|
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 | 2026-07-26 09:08:19 | 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 | 2026-07-26 09:08:24 | 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 | 2026-07-26 09:08:23 | 0 |
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