Tools   Select Another Resource Report Type

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   

•   Source: SciCrunch Registry
  

https://github.com/walaj/SeqLib

Software C++ htslib/bwa-mem/fermi interface for interrogating sequence data

Proper citation: SeqLib (RRID:SCR_024091) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

https://github.com/SciLifeLab/TIDDIT

Software tool as structural variant calling.

Proper citation: tiddit (RRID:SCR_024361) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

https://github.com/mateidavid/nanocall

Software basecaller for Oxford Nanopore Technologies sequencing data. Oxford Nanopore Basecaller.

Proper citation: Nanocall (RRID:SCR_024124) Copy   

•   Source: SciCrunch Registry
  

https://github.com/torognes/swarm

Software tool as clustering method for amplicon-based studies.

Proper citation: swarm (RRID:SCR_024358) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

http://segway.hoffmanlab.org/

The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. The method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. Segway uses the Graphical Models Toolkit (GMTK) for efficient DBN inference. The software has extensive documentation and was designed from the outset with external users in mind.

Proper citation: Segway - a way to segment the genome (RRID:SCR_004206) Copy   

•   Source: SciCrunch Registry
  

https://github.com/telatin/covtobed

Software tool to generate BED coverage tracks from BAM files.

Proper citation: covtobed (RRID:SCR_023998) Copy   

•   Source: SciCrunch Registry
  

http://bioinfo.unl.edu/gramalign.php

Software tool as time efficient progressive Multiple Sequence Alignment algorithm. Sequence distance estimation step is determined by the natural grammar present in nucleotide and amino acid sequences.

Proper citation: GramAlign (RRID:SCR_024032) Copy   

•   Source: SciCrunch Registry
  

https://gitlab.com/rki_bioinformatics/IDeFIX

Software tool for demultiplexing Illumina NGS data. Reports inconsistencies between the raw data and the Sample Sheet, checks for duplicates of indices/ index combinations in the latter and removes unwanted characters from it. Creates an IDeFIX_Report.csv containing the indices/ index combinations from the raw data and their abundance as well as their count in the Sample Sheet and the corresponding Index ID(s).

Proper citation: IDeFIX (RRID:SCR_024033) Copy   

•   Source: SciCrunch Registry
  

https://github.com/lbcb-sci/graphmap2

Software tool as splice aware RNA-seq mapper for long reads produced by Pacific Biosciences and Oxford Nanopore devices

Proper citation: GraphMap2 (RRID:SCR_024035) Copy   

•   Source: SciCrunch Registry
  

https://github.com/genouest/biomaj

Software workflow engine dedicated to data synchronization and processing. Software automates the update cycle and the supervision of the locally mirrored databank repository.

Proper citation: BioMAJ (RRID:SCR_023983) Copy   

•   Source: SciCrunch Registry
  

https://www.gnumed.de/documentation/

Software to build Electronic Medical Record in multiple languages to assist and improve longitudinal care specifically in ambulatory settings.Useful to anyone documenting the health of patients including,doctors, physical therapists, occupational therapists,acupuncturists, nurses, psychologists.

Proper citation: GNUmed (RRID:SCR_024029) Copy   

•   Source: SciCrunch Registry
  

http://ruby.chemie.uni-freiburg.de/~martin/chemtool/

Software tool for drawing organic molecules. Runs under the X Window System using the GTK widget set. Used for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11.

Proper citation: Chemtool (RRID:SCR_023992) Copy   

•   Source: SciCrunch Registry