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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
https://gitlab.com/andreas.andrusch/paipline
Software Python program to search for pathogen nucleic acid sequences in NGS datasets.Used for pathogen identification in metagenomic and clinical next generation sequencing samples.
Proper citation: PAIPline (RRID:SCR_024151) Copy
https://sourceforge.net/projects/pipasic/
Software tool for similarity and expression correction for strain level identification and quantification in metaproteomics. Peptide intensity weighted proteome abundance similarity correction tool to correct identification and spectral counting based quantification results. Pipasic has distinct advantages over approaches only regarding unique peptides or aggregating results to the lowest common ancestor.
Proper citation: pipasic (RRID:SCR_024165) Copy
https://github.com/BU-ISCIII/plasmidID
Software mapping based, assembly assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification. Computational pipeline implemented in BASH that maps Illumina reads over plasmid database sequences.
Proper citation: PlasmidID (RRID:SCR_024166) Copy
https://github.com/PacificBiosciences/kineticsTools
Software tools for detecting DNA modifications from single molecule, real-time sequencing data. This tool implements the P_ModificationDetection module in SMRT� Portal, used by the RS_Modification_Detection and RS_Modifications_and_Motif_Detection protocol.
Proper citation: kineticsTools (RRID:SCR_024049) Copy
http://www.biolchem.ucla.edu/labs/ernst/ChromImpute/
Software tool for large scale systematic epigenome imputation. ChromImpute takes existing compendium of epigenomic data and uses it to predict signal tracks for mark-sample combinations not experimentally mapped or to generate a potentially more robust version of data sets that have been mapped experimentally.
Proper citation: ChromImpute (RRID:SCR_023990) Copy
Open source, software cross-platform library that provides suite of software tools for image analysis.ITK builds on proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.
Proper citation: Insight Toolkit (RRID:SCR_024040) Copy
https://github.com/HadrienG/InSilicoSeq
Software tool as sequencing simulator producing realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome.
Proper citation: InSilicoSeq (RRID:SCR_024041) Copy
https://bitbucket.org/genomicepidemiology/resfinder
Software tool identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria. Used for identification of acquired antimicrobial resistance genes in whole-genome data.
Proper citation: resfinder (RRID:SCR_024314) Copy
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