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https://github.com/PapenfussLab/bionix
Software tool for reproducible bioinformatics that unifies workflow engines, package managers, and containers. Implemented as lightweight library on top of Nix deployment system. Bioinformatics workflows in functional Nix language.
Proper citation: BioNix (RRID:SCR_017662) Copy
https://github.com/hariszaf/pema
Software as flexible pipeline for environmental DNA metabarcoding analysis of 16S/18S rRNA, ITS and COI marker genes. Performs reads’ pre-processing, clustering to (M)OTUs and taxonomy assignment for 16S rRNA and COI marker gene data. Allows users to explore alternative algorithms for specific steps of pipeline without need of complete re-execution.
Proper citation: PEMA (RRID:SCR_017676) Copy
https://bitbucket.org/genomicepidemiology/kma/src/master/
Software mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.Used for aligning high quality reads against highly redundant databases, where unique matches often does not exist. Works for long low quality reads as well, such as those from Nanopore. Non-unique matches are resolved using the "ConClave" sorting scheme, and a consensus sequence are outputtet in addition to other common attributes, based on users demands.
Proper citation: KMA (RRID:SCR_024054) Copy
Software parallel local alignment search tool for database comparison. NGS sequence similarity search tool providing significant accelerations of seeds based heuristic comparison methods.
Proper citation: PLAST (RRID:SCR_024170) Copy
https://github.com/ahmedmoustafa/JAligner
Open source software Java implementation of the Needleman�Wunsch and Smith-Waterman algorithms for biological pairwise sequence alignment with the affine gap penalty model.
Proper citation: JAligner (RRID:SCR_024050) Copy
https://seqan.github.io/lambda/
Software tool as local aligner optimized for many query sequences and searches in protein space. It is compatible to BLAST, but much faster than BLAST and many other comparable tools.
Proper citation: Lambda (RRID:SCR_024052) Copy
https://github.com/cboursnell/crb-blast
Software tool for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation.
Proper citation: crb-blast (RRID:SCR_024325) Copy
https://www.tau.ac.il/~itaymay/cp/rate4site.html
Software tool for detecting conserved amino-acid sites by computing relative evolutionary rate for each site in multiple sequence alignment. Used for identification of functional regions in proteins.
Proper citation: Rate4Site (RRID:SCR_024222) Copy
Software for alignment free sequence comparison. Uses pattern of care and don't care positions. Compares frequencies of spaced words according to pre-defined pattern.
Proper citation: spaced (RRID:SCR_024345) Copy
Pattern matching grammar language and set of tools to search pattern in sequence nucleic or proteic.
Proper citation: Logol (RRID:SCR_024104) Copy
https://www.sofa-framework.org/
Open source software framework targeting at real-time simulation, with emphasis on medical simulation.
Proper citation: sofa-apps (RRID:SCR_024346) Copy
https://gitlab.com/rki_bioinformatics/purple
Software tool for selecting target specific peptide candidates directly from given proteome sequence data.
Proper citation: purple (RRID:SCR_024183) Copy
http://bioinf.spbau.ru/sibelia
Software comparative genomics tool to assist biologists in analysing genomic variations that correlate with pathogens, or genomic changes that help microorganisms adapt in different environments. Used for evolutionary and genome rearrangement studies for multiple strains of microorganisms.
Proper citation: sibelia (RRID:SCR_024336) Copy
https://sibsim4.sourceforge.net/
Software tool designed to align expressed DNA sequence with genomic sequence, allowing for introns.
Proper citation: sibsim4 (RRID:SCR_024338) Copy
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
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
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
http://prodata.swmed.edu/pcma/pcma.php
Software tool for multiple sequence alignment based on profile consistency. Used to construct multiple sequence alignment given set of protein sequences.
Proper citation: PCMA (RRID:SCR_024156) Copy
https://github.com/brettc/partitionfinder
Software Python program to discover optimal partitioning schemes for DNA sequences.Used for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data.
Proper citation: PartitionFinder (RRID:SCR_024157) Copy
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
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