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https://github.com/najoshi/sabre

Software tool to demultiplex barcoded reads into separate files. Works on both single-end and paired-end data in fastq format. Used in next generation sequencing to analyze a broad range of data.

Proper citation: sabre (RRID:SCR_011843) Copy   

•   Source: SciCrunch Registry

http://www.molecularevolution.org/software/genomics/velvet

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package as de novo genomic assembler for short read sequencing technologies using de Bruijn graphs. Takes in short read sequences, removes errors, then produces high quality unique contigs, retrieves repeated areas between contigs. Can leverage very short reads in combination with read pairs to produce useful assemblies. Operating system Unix/Linux., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Velvet (RRID:SCR_010755) Copy   

•   Source: SciCrunch Registry

http://bio-bwa.sourceforge.net/

Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.

Proper citation: BWA (RRID:SCR_010910) Copy   

•   Source: SciCrunch Registry

https://github.com/FRED-2/OptiType

Software tool for precision HLA typing from next generation sequencing data.

Proper citation: OptiType (RRID:SCR_022279) Copy   

•   Source: SciCrunch Registry

http://rrwick.github.io/Bandage/

Software tool for visualising de novo assembly graphs. By displaying connections which are not present in contigs file, opens up new possibilities for analysing de novo assemblies. Used for interactive visualization of de novo genome assemblies.

Proper citation: Bandage (RRID:SCR_022772) Copy   

•   Source: SciCrunch Registry

http://www.mricro.com

Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.

Proper citation: MRIcron (RRID:SCR_002403) Copy   

•   Source: SciCrunch Registry

https://github.com/qmarcou/IGoR/

C++ software designed to infer V(D)J recombination related processes from sequencing data.

Proper citation: IGoR (RRID:SCR_024053) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/paulklemm_PHD/proteinortho

Software tool to detect orthologous genes within different species. Stand-alone tool for large datasets for orthology analysis.

Proper citation: Proteinortho (RRID:SCR_024177) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/genomicepidemiology/kmerresistance/src/master/

Software tool to correlate mapped genes with the predicted species of WGS samples, where this allows for identification of genes in samples which have been poorly sequenced or high accuracy predictions for samples with contamination. KmerResistance has one dependency, namely KMA to perform the mapping, which is also freely available.

Proper citation: KmerResistance (RRID:SCR_024058) Copy   

•   Source: SciCrunch Registry

https://rostlab.org/owiki/index.php/PROFisis

Software tool that identifies interacting residues from sequence alone. Developed using transient protein�protein interfaces from complexes of experimentally known 3D structures.

Proper citation: PROFisis (RRID:SCR_024179) Copy   

•   Source: SciCrunch Registry

http://proda.stanford.edu/

Software for multiple alignment of protein sequences with repeated and shuffled elements.Used for automated detection and alignment of homologous regions in collections of proteins with arbitrary domain architectures.

Proper citation: ProDA (RRID:SCR_024171) Copy   

•   Source: SciCrunch Registry

https://github.com/klebgenomics/Kleborate

Software tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for MLST sequence type, species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.), ICEKp associated virulence loci (yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA)), virulence plasmid associated loci (salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2)), antimicrobial resistance determinants (acquired genes, SNPs, gene truncations and intrinsic ?-lactamases), and K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive.

Proper citation: Kleborate (RRID:SCR_024051) Copy   

•   Source: SciCrunch Registry

https://ukoethe.github.io/vigra/

Software image processing and analysis library that puts its main emphasis on customizable algorithms and data structures. VIGRA is especially strong for multi-dimensional images. By using template techniques similar to those in the C++ Standard Template Library, you can easily adapt any VIGRA component to the needs of your application, without thereby giving up execution speed. As of version 1.7.1, VIGRA also provides extensive Python bindings on the basis of the popular numpy framework.

Proper citation: VIGRA (RRID:SCR_024100) Copy   

•   Source: SciCrunch Registry

https://github.com/biocore/pynast

Software tool for aligning sequences to template alignment.

Proper citation: pynast (RRID:SCR_024189) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.org/patristic/

Software Java program for calculating patristic distances and graphically comparing the components of genetic change.

Proper citation: Patristic (RRID:SCR_024154) Copy   

•   Source: SciCrunch Registry

https://docs.igdiscover.se/en/stable/

Software to analyze antibody repertoires and discover new V genes from high-throughput sequencing reads.Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: IgDiscover (RRID:SCR_024037) Copy   

•   Source: SciCrunch Registry

https://data.broadinstitute.org/alkesgroup/BOLT-LMM/

Software statistical tool for identifying genetic associations. Used for genome wide association studies in large cohorts.

Proper citation: BOLT-LMM (RRID:SCR_023978) Copy   

•   Source: SciCrunch Registry

https://github.com/sanger-pathogens/iva

Software tool as de novo assembler designed to assemble virus genomes that have no repeat sequences,using Illumina read pairs sequenced from mixed populations at extremely high and variable depth.

Proper citation: IVA (RRID:SCR_024044) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinfo-ut/PlasmidSeeker

Software tool as k-mer based program for identification of known plasmids from whole genome sequencing reads. Used for identification of known plasmids from bacterial whole genome sequencing reads.

Proper citation: PlasmidSeeker (RRID:SCR_024167) Copy   

•   Source: SciCrunch Registry

http://contra.stanford.edu/contrafold/

Software novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. Used for sequence prediction.

Proper citation: CONTRAfold (RRID:SCR_023994) Copy   

•   Source: SciCrunch Registry