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https://github.com/WGS-TB/MentaLiST

Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes.

Proper citation: MentaLiST (RRID:SCR_016469) Copy   

•   Source: SciCrunch Registry

https://cistem.org/

Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.

Proper citation: cisTEM (RRID:SCR_016502) Copy   

•   Source: SciCrunch Registry

https://github.com/fbreitwieser/pavian

Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome.

Proper citation: Pavian (RRID:SCR_016679) Copy   

•   Source: SciCrunch Registry

http://www.ccb.jhu.edu/software/centrifuge/

Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers.

Proper citation: Centrifuge Classifier (RRID:SCR_016665) Copy   

•   Source: SciCrunch Registry

https://tbportals.niaid.nih.gov

Web based open access platform for global drug resistant tuberculosis data sharing and analysis. The NIAID TB Portals program and consortium of clinicians and scientists from countries with a heavy burden of TB, especially drug resistant TB, to collect TB data.

Proper citation: TB PORTALS (RRID:SCR_016594) Copy   

•   Source: SciCrunch Registry

https://nmrprocflow.org

Software as graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics.

Proper citation: NMRProcFlow (RRID:SCR_016592) Copy   

•   Source: SciCrunch Registry

http://ecogenomics.github.io/CheckM/

Software tool to assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes by using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes.

Proper citation: CheckM (RRID:SCR_016646) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/projects/genotyping/formpage.cgi

Web tool to identify the genotype of a viral sequence. A window is slid along the query sequence and each window is compared by BLAST to each of the reference sequences for a particular virus.

Proper citation: Genotyping (RRID:SCR_016645) Copy   

•   Source: SciCrunch Registry

https://github.com/iychoi/libra

Hadoop based tool for massive comparative metagenomics analysis. Compute the similarity between metagenomic samples.

Proper citation: Libra (RRID:SCR_016608) Copy   

•   Source: SciCrunch Registry

https://pachterlab.github.io/kallisto/about

Software tool for quantifying abundances of transcripts from RNA-Seq data or target sequences using high-throughput sequencing reads.

Proper citation: kallisto (RRID:SCR_016582) Copy   

•   Source: SciCrunch Registry

http://paintmychromosomes.com/

Software tool as algorithm for identifying population structure using dense sequencing data. Can perform model based Bayesian clustering on large datasets, including full resequencing data.

Proper citation: fineSTRUCTURE (RRID:SCR_018170) Copy   

•   Source: SciCrunch Registry

https://github.com/lmcinnes/umap

Software package as dimension reduction technique that can be used for visualization similar to t-SNE, but also for general non-linear dimension reduction. Used for dimensionality reduction for visualizing single-cell data.

Proper citation: Umap (RRID:SCR_018217) Copy   

•   Source: SciCrunch Registry

https://github.com/yousra291987/ChiCMaxima

Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling.

Proper citation: ChiCMaxima (RRID:SCR_018178) Copy   

•   Source: SciCrunch Registry

https://github.com/esctrionsit/snphub

Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data.

Proper citation: SnpHub (RRID:SCR_018177) Copy   

•   Source: SciCrunch Registry

https://github.com/BUStools/bustools/

Software tool for manipulating BUS files for single cell RNA-Seq datasets. Used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks.

Proper citation: Bustools (RRID:SCR_018210) Copy   

•   Source: SciCrunch Registry

https://github.com/santeripuranen/SpydrPick

Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree.

Proper citation: SpydrPick (RRID:SCR_018176) Copy   

•   Source: SciCrunch Registry

http://crispr.dbcls.jp/

Software for designing CRISPR/Cas guide RNA with reduced off target sites. Used for rational design of CRISPR/Cas target. Web server for selecting rational CRISPR/Cas targets from input sequence. Server currently incorporates genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast.

Proper citation: CRISPRdirect (RRID:SCR_018186) Copy   

•   Source: SciCrunch Registry

https://github.com/WangHYLab/fcirc

Software Python pipeline for linear and circular RNAs of known fusions exploration. Pipeline for exploring linear transcripts and circRNAs of known fusions based on RNA-Seq data. Known fusion genes are from multiple databases like COSMIC, ChimerDB, TicDB, FARE-CAFE and FusionCancer or user-added gene-pairs.

Proper citation: Fcirc (RRID:SCR_018090) Copy   

•   Source: SciCrunch Registry

http://www.prc.boun.edu.tr/appserv/prc/hingeprot/index.html

Web server for predicting rigid protein parts and flexible hinge regions connecting them in native topology of protein chains by employing elastic network (EN) models. Automated prediction of hinges in protein structures.

Proper citation: HingeProt (RRID:SCR_018136) Copy   

•   Source: SciCrunch Registry

http://compbio.mit.edu/ChromHMM/

Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations.

Proper citation: ChromHMM (RRID:SCR_018141) Copy   

•   Source: SciCrunch Registry