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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
Comprehensive antibiotic resistance database. Bioinformatic database of resistance genes, their products and associated phenotypes.
Proper citation: CARD (RRID:SCR_023995) 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
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
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.
Proper citation: CamiTK (RRID:SCR_023984) Copy
https://github.com/aberer/RogueNaRok
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.
Proper citation: roguenarok (RRID:SCR_024316) Copy
http://faculty.washington.edu/tathornt/software/ROADTRIPS2/
Software C program that performs single SNP, case control association testing in samples with partially or completely unknown population and pedigree structure.
Proper citation: roadtrips (RRID:SCR_024318) Copy
https://github.com/brentp/vcfanno
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.
Proper citation: vcfanno (RRID:SCR_024372) Copy
https://github.com/walaj/SeqLib
Software C++ htslib/bwa-mem/fermi interface for interrogating sequence data
Proper citation: SeqLib (RRID:SCR_024091) Copy
https://bitbucket.org/genomicepidemiology/virulencefinder
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.
Proper citation: VirulenceFinder (RRID:SCR_024371) Copy
http://www.bioinformatics.org/strap/
Software tool as Intuitive Editor for annotated multiple Sequence and Structure Alignments.
Proper citation: strap-base (RRID:SCR_024351) Copy
https://github.com/nanoporetech/qcat
Software Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.
Proper citation: qcat (RRID:SCR_024195) Copy
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