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https://github.com/rrwick/Filtlong
Software tool for filtering long reads by quality.Can take set of long reads and produce smaller, better subset. Uses both read length and read identity when choosing which reads pass the filter.
Proper citation: Filtlong (RRID:SCR_024020) Copy
https://github.com/qmarcou/IGoR/
C++ software designed to infer V(D)J recombination related processes from sequencing data.
Proper citation: IGoR (RRID:SCR_024053) Copy
https://gitlab.com/paulklemm_PHD/proteinortho
Software tool to detect orthologous genes within different species. Stand-alone tool for large datasets for orthology analysis.
Proper citation: Proteinortho (RRID:SCR_024177) Copy
https://bitbucket.org/genomicepidemiology/kmerresistance/src/master/
Software tool to correlate mapped genes with the predicted species of WGS samples, where this allows for identification of genes in samples which have been poorly sequenced or high accuracy predictions for samples with contamination. KmerResistance has one dependency, namely KMA to perform the mapping, which is also freely available.
Proper citation: KmerResistance (RRID:SCR_024058) Copy
http://www.bioinformatics.org/patristic/
Software Java program for calculating patristic distances and graphically comparing the components of genetic change.
Proper citation: Patristic (RRID:SCR_024154) Copy
https://github.com/bioinfo-ut/PlasmidSeeker
Software tool as k-mer based program for identification of known plasmids from whole genome sequencing reads. Used for identification of known plasmids from bacterial whole genome sequencing reads.
Proper citation: PlasmidSeeker (RRID:SCR_024167) Copy
https://github.com/babinyurii/recan
Software tool as genetic distance plotting for recombination events analysis.
Proper citation: recan (RRID:SCR_024317) Copy
https://github.com/mourisl/Lighter
Software tool as kmer-based error correction method for whole genome sequencing data. Lighter uses sampling rather than counting to obtain set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.
Proper citation: Lighter (RRID:SCR_024095) Copy
http://www.nematodes.org/bioinformatics/trace2dbEST/
Software tool to process raw sequenceing chromatograph trace files from EST projects into quality checked sequences, ready for submission to dbEST.
Proper citation: trace2dbEST (RRID:SCR_024386) Copy
https://github.com/sina-cb/Tn-seqExplorer
Software package written in Java for analysis of high-throughput sequencing data of transposon mutant libraries.Reads the alignment and the gene annotation, and provides the user with set of tools to investigate data and identify possibly essential or advantageous genes as those that contain significantly low counts of transposon insertions.
Proper citation: Tn-seq explorer (RRID:SCR_024387) Copy
http://saclab.tamu.edu/essentiality/transit/
Software tool for Himar1 TnSeq analysis.Provides graphical interface to three different statistical methods for analyzing TnSeq data. Used for identifying essential genes in individual datasets as well as comparative analysis between conditions.
Proper citation: TRANSIT (RRID:SCR_024389) Copy
Software tool to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. Allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Computes pairwise maximum likelihood distances as well as branch lengths for user specified trees.Conducts statistical tests on the data set.
Proper citation: TREE-PUZZLE (RRID:SCR_024382) Copy
https://bitbucket.org/Glouvel/metabit/wiki/Home
Software pipeline for metagenomic and taxonomical analysis from shotgun sequencing.
Proper citation: metaBIT (RRID:SCR_024111) Copy
https://qtlreaper.sourceforge.net/
Software, written in C and compiled as Python module, for rapidly scanning microarray expression data for Quantitative Trait Locies. Searches for association between each expression trait and all genotypes and evaluates that association by permutation test. Performs bootstrap resampling to estimate confidence region for location of putative QTL.
Proper citation: qtlreaper (RRID:SCR_024199) Copy
https://mhap.readthedocs.io/en/stable/
Software tool as reference implementation of probabilistic sequence overlapping algorithm. Used to detect overlaps between noisy long-read sequence data.
Proper citation: MHAP (RRID:SCR_024113) Copy
https://github.com/GATB/MindTheGap
Software tool to perform detection and assembly of DNA insertion variants in NGS read datasets with respect to reference genome.Used to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome.
Proper citation: MindTheGap (RRID:SCR_024115) Copy
https://jydu.github.io/maffilter/
Software tool for analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files. Despite various filtering options and format conversion tools, MafFilter can compute a wide range of statistics including phylogenetic trees, nucleotide diversity, inferrence of selection, etc.
Proper citation: MafFilter (RRID:SCR_024105) Copy
https://sparta.readthedocs.io/en/latest/
Software workflow aimed at analyzing single-end Illumina RNA-seq data. The software is supported on Windows, Mac OS X, and Linux platforms.
Proper citation: sparta (RRID:SCR_024349) Copy
https://github.com/Pas-Kapli/mptp
Software tool for single locus species delimitation. Implements fast method to compute the ML delimitation from inferred phylogenetic tree of the samples.Used to handle very large biodiversity datasets.
Proper citation: mPTP (RRID:SCR_024121) Copy
Software tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses.
Proper citation: MRtrix3 (RRID:SCR_024123) Copy
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