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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
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://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
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://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://johnhommer.com/academic/code/aghermann
Sotware tool designed to run Process S simulations on Slow Wave Activity profiles from human EEG recordings.Produces set of sleep homeostat parameters which can be used to describe and differentiate individual sleepers, such as short vs long sleepers, early vs late, etc.Sleep research experiment manager, with facility for reading, displaying, and manual and semi-automatic scoring EEG recordings in edf format; conventional PSD and EEG Microcontinuity profiles; artifact detection; Independent Component Analysis; basic sleep analysis NREM-REM cycle detection.
Proper citation: Aghermann (RRID:SCR_023965) 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/gem-pasteur/macsyfinder
Software tool to mine genomes for molecular systems with Application to CRISPR-Cas Systems. Detection of macromolecular systems in protein datasets using systems modelling and similarity search.
Proper citation: MacSyFinder (RRID:SCR_024106) Copy
https://github.com/SciLifeLab/TIDDIT
Software tool as structural variant calling.
Proper citation: tiddit (RRID:SCR_024361) Copy
https://github.com/Adamtaranto/Yanagiba
Software tool to filter and slice Nanopore reads which have been basecalled with Albacore.
Proper citation: Yanagiba (RRID:SCR_024362) Copy
https://github.com/mateidavid/nanocall
Software basecaller for Oxford Nanopore Technologies sequencing data. Oxford Nanopore Basecaller.
Proper citation: Nanocall (RRID:SCR_024124) Copy
https://github.com/torognes/swarm
Software tool as clustering method for amplicon-based studies.
Proper citation: swarm (RRID:SCR_024358) Copy
http://www.bioinfor.com/zoom/general/overview.html
Software to map the Illumina/Solexa reads of 15x coverage of a human genome to the reference human genome in one CPU-day, allowing two mismatches, at full sensitivity.
Proper citation: ZOOM (RRID:SCR_002175) Copy
https://www.integromics.com/omicsoffice-for-ngs/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software for secondary and tertiary analysis of Next Generation Sequencing (NGS) data.
Proper citation: OmicsOffice for NGS SeqSolve (RRID:SCR_001222) Copy
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