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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.
Proper citation: ABACAS (RRID:SCR_015852) Copy
http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMAINATRIX
Software for protein domain search. It is a part of Embassy software package.
Proper citation: DOMAINATRIX (RRID:SCR_016084) Copy
https://git.metabarcoding.org/obitools/ecopcr/wikis/home
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.
Proper citation: Ecopcr (RRID:SCR_016082) Copy
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.
Proper citation: QGIS (RRID:SCR_018507) Copy
https://github.com/rbutleriii/Clinotator
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.
Proper citation: Clinotator (RRID:SCR_016054) Copy
https://metacpan.org/dist/Bio-ASN1-EntrezGene
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.
Proper citation: Bio-ASN1-EntrezGene (RRID:SCR_024056) Copy
https://metacpan.org/dist/AcePerl
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.
Proper citation: AcePerl (RRID:SCR_024057) Copy
https://odelaneau.github.io/shapeit4/
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.
Proper citation: shapeit4 (RRID:SCR_024335) Copy
https://www.cs.cmu.edu/~ckingsf/software/sailfish/
Software tool that implements novel, alignment free algorithm for estimation of isoform abundances directly from set of reference sequences and RNA-seq reads.
Proper citation: sailfish (RRID:SCR_024326) Copy
https://github.com/fenderglass/Ragout/
Software tool for chromosome level scaffolding using multiple references. Given initial assembly fragments and one or multiple related references it produces chromosome scale assembly.
Proper citation: ragout (RRID:SCR_024206) Copy
https://metacpan.org/dist/Bio-SamTools
Software Perl interface to SamTools library for DNA sequencing.
Proper citation: Bio-SamTools (RRID:SCR_024066) Copy
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.
Proper citation: skesa (RRID:SCR_024341) Copy
https://github.com/phac-nml/sistr_cmd
SISTR command-line tool. Open web accessible tool for rapidly typing and subtyping draft salmonella genome assemblies.
Proper citation: sistr (RRID:SCR_024342) Copy
https://metacpan.org/dist/Bio-SCF
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.
Proper citation: Bio-SCF (RRID:SCR_024068) Copy
https://github.com/COMBINE-lab/pufferfish
Software tool implementing novel indexing data structure for compacted de Bruijn graph and colored compacted de Bruijn graph.
Proper citation: pufferfish (RRID:SCR_024184) Copy
http://bioinformatics.org/biococoa/
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.
Proper citation: BioCocoa (RRID:SCR_023977) Copy
http://biblatex-biber.sourceforge.net/
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.
Proper citation: Biber (RRID:SCR_023973) Copy
https://github.com/davidsoergel/rtax/
Software tool for rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene.
Proper citation: rtax (RRID:SCR_024320) Copy
https://github.com/narunlifescience/runcircos-gui
GUI tool to run circos
Proper citation: runcircos-gui (RRID:SCR_024321) Copy
https://autodock.scripps.edu/resources/raccoon/
Software graphical interface for preparing AutoDock virtual screenings.Automates some of the most common operations performed when preparing virtual screening.
Proper citation: raccoon (RRID:SCR_024201) Copy
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