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https://chlorobox.mpimp-golm.mpg.de/geseq.html

Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes.

Proper citation: GeSeq (RRID:SCR_017336) Copy   

•   Source: SciCrunch Registry

https://github.com/taborlab/FlowCal

Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots.

Proper citation: FlowCal (RRID:SCR_018140) Copy   

•   Source: SciCrunch Registry

https://github.com/wdecoster/nanofilt

Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data.

Proper citation: NanoFilt (RRID:SCR_016966) Copy   

•   Source: SciCrunch Registry

https://github.com/mandricigor/ScaffMatch

Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes.

Proper citation: ScaffMatch (RRID:SCR_017025) Copy   

•   Source: SciCrunch Registry

https://github.com/ComparativeGenomicsToolkit/hal/tree/master/synteny

Software tool as conserved synteny block construction method for multiple whole-genome alignments. Implementation of DAG-based for reconstruction of synteny blocks from genome alignment.

Proper citation: halSynteny (RRID:SCR_018127) Copy   

•   Source: SciCrunch Registry

https://github.com/Brazelton-Lab/seq-annot

Software Python package for annotating and counting genomic features in genomes and metagenomes. Software tools to facilitate annotation and comparison of genomes and metagenomes.

Proper citation: seq-annot (RRID:SCR_018731) Copy   

•   Source: SciCrunch Registry

https://github.com/almorlio/CiLiQuant

Software tool to separate junction reads based on their linear or circular origin. Only non ambiguous junction reads are used to compare relative linear and circular transcript abundance.

Proper citation: CiLiQuant (RRID:SCR_019319) Copy   

•   Source: SciCrunch Registry

https://qupath.github.io/

Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images.

Proper citation: QuPath (RRID:SCR_018257) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-EUtilities

Software package which interacts with and retrieves data from NCBI's eUtils. This distribution encompasses low-level API for interacting with (and storing) information from NCBI's eUtils interface. See Bio::DB::EUtilities for the query API to retrieve data from NCBI, and Bio::Tools::EUtilities for the general class storage system. Note this may change to utilize the XML schema for each class at some point, though we will attempt to retain current functionality for backward compatibility unless this becomes problematic.

Proper citation: Bio-EUtilities (RRID:SCR_024064) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-Tools-Run-Alignment-Clustalw

Software package for performing multiple sequence alignment from set of unaligned sequences and/or sub-alignments by means of the clustalw program.

Proper citation: Bio-Tools-Run-Alignment-Clustalw (RRID:SCR_024067) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-Tools-Phylo-PAML

Software package used to parse output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio-Tools-Run-Phylo-PAML modules to actually run some of the PAML programs, but this module is only useful to parse the output.

Proper citation: Bio-Tools-Phylo-PAML (RRID:SCR_024069) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-Graphics

Software package to generate GD images of Bio::Seq objects.

Proper citation: Bio-Graphics (RRID:SCR_024061) Copy   

•   Source: SciCrunch Registry

https://github.com/genouest/biomaj-cli

Software package to use BioMAJ providing biomaj-cli.

Proper citation: CLI for BioMAJ (RRID:SCR_023980) Copy   

•   Source: SciCrunch Registry

https://github.com/GATB/bcalm

Software tool for constructing compacted de Bruijn graph from sequencing data.Parallel algorithm that distributes the input based on minimizer hashing technique, allowing for good balance of memory usage throughout its execution.

Proper citation: BCALM 2 (RRID:SCR_023975) Copy   

•   Source: SciCrunch Registry

https://github.com/gpertea/gclib

Software genomic C++ library of reusable code for bioinformatics projects.Provides core collection of data structures, trying to avoid unnecessary code dependencies of other heavy libraries, while minimizing build time.

Proper citation: GCLib (RRID:SCR_024028) Copy   

•   Source: SciCrunch Registry

https://github.com/dutilh/CAT

Software pipeline for taxonomic classification of contigs and metagenome-assembled genomes. Contig Annotation Tool and Bin Annotation Tool for the taxonomic classification of long DNA sequences and metagenome assembled genomes of both known and unknown microorganisms, as generated by contemporary metagenomics studies.

Proper citation: CAT and BAT (RRID:SCR_023988) Copy   

•   Source: SciCrunch Registry

https://github.com/WorkflowConversion/CTDConverter

Software Python scripts to convert CTD files into other formats such as Galaxy, CWL.

Proper citation: CTDConverter (RRID:SCR_024007) Copy   

•   Source: SciCrunch Registry

https://freeimage.sourceforge.io/

Open Source software library for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications.

Proper citation: FreeImage (RRID:SCR_024022) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinfo-ut/GenomeTester4

Software toolkit for performing set operations - union, intersection and complement on k-mer lists.

Proper citation: GenomeTester4 (RRID:SCR_024026) Copy   

•   Source: SciCrunch Registry

http://gdcm.sourceforge.net/

GDCM includes file format definition and network communications protocol, both of which should be extended to provide full set of tools for researcher or small medical imaging vendor to interface with existing medical database.Implementation of DICOM standard designed to be open source so that researchers may access clinical data directly.

Proper citation: GDCM (RRID:SCR_024027) Copy   

•   Source: SciCrunch Registry