PathoGiST v0.3.6 – Clustering Pathogen Isolates by combining multiple Genotyping Signals

PathoGiST v0.3.6

:: DESCRIPTION

PathOGiST is an algorithmic framework for clustering bacterial isolates by leveraging multiple genotypic signals and calibrated thresholds.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • conda

:: DOWNLOAD

PathOGiST

:: MORE INFORMATION

Citation

Katebi M. et al. (2020)
PathOGiST: A Novel Method for Clustering Pathogen Isolates by Combining Multiple Genotyping Signals.
Algorithms for Computational Biology. AlCoB 2020. Lecture Notes in Computer Science, vol 12099. Springer, Cham. https://doi.org/10.1007/978-3-030-42266-0_9

Straglr v1.1.1 – Short-tandem Repeat Genotyping using long Reads

Straglr v1.1.1

:: DESCRIPTION

Straglr is a new software tool for targeted genotyping and repeat expansion detection

::DEVELOPER

BC Cancer Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

Straglr

:: MORE INFORMATION

Citation

Chiu R, Rajan-Babu IS, Friedman JM, Birol I.
Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences.
Genome Biol. 2021 Aug 13;22(1):224. doi: 10.1186/s13059-021-02447-3. PMID: 34389037; PMCID: PMC8361843.

RADtyping 1.3.0 – de novo RAD Genotyping in Mapping Populations

RADtyping 1.3.0

:: DESCRIPTION

RADtyping is a user-defined perl procedure for performing de novo RAD genotyping in mapping populations. It can deal with both single-end and paired-end RAD sequencing data.

::DEVELOPER

RADtyping team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • Perl

:: DOWNLOAD

 RADtyping

:: MORE INFORMATION

Citation

PLoS One. 2013 Nov 21;8(11):e79960. doi: 10.1371/journal.pone.0079960. eCollection 2013.
RADtyping: an integrated package for accurate de novo codominant and dominant RAD genotyping in mapping populations.
Fu X1, Dou J, Mao J, Su H, Jiao W, Zhang L, Hu X, Huang X, Wang S, Bao Z.

HnaTyping 1.0.1 – HNA Genotyping From WGS

HnaTyping 1.0.1

:: DESCRIPTION

HnaTyping is a software for genotyping of human neutrophil antigens (HNA) from whole genome sequencing data

::DEVELOPER

Frank Hsueh-Ting Chu

:: SCREENSHOTS

HnaTyping

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 HnaTyping

:: MORE INFORMATION

Citation

BMC Med Genomics. 2013 Sep 12;6:31. doi: 10.1186/1755-8794-6-31.
Genotyping of human neutrophil antigens (HNA) from whole genome sequencing data.
Chu HT1, Lin H, Tsao TT, Chang CF, Hsiao WW, Yeh TJ, Chang CM, Liu YW, Wang TY, Yang KC, Chen TJ, Chen JC, Chen KC, Kao CY.

HPV-EM 1.0.2 – HPV Detection and Genotyping tool

HPV-EM 1.0.2

:: DESCRIPTION

HPV-EM is an HPV genotyping tool that utilizes an expectation maximization algorithm to identify the presence of HPV genotypes in a sample from RNA-seq data

::DEVELOPER

The Zhang Translational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows
  • Python

:: DOWNLOAD

HPV-EM

:: MORE INFORMATION

Citation

Inkman MJ, Jayachandran K, Ellis TM, Ruiz F, McLellan MD, Miller CA, Wu Y, Ojesina AI, Schwarz JK, Zhang J.
HPV-EM: an accurate HPV detection and genotyping EM algorithm.
Sci Rep. 2020 Aug 31;10(1):14340. doi: 10.1038/s41598-020-71300-7. PMID: 32868873; PMCID: PMC7459114.

snpQC – Quality Control of Illumina SNP Genotyping Array data

snpQC

:: DESCRIPTION

snpQC is an R based fully automated pipeline for preprocessing, storage and quality control of Illumina SNP data.

::DEVELOPER

Cedric Gondro

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • R

:: DOWNLOAD

  snpQC

:: MORE INFORMATION

Citation

Anim Genet. 2014 Oct;45(5):758-61. doi: 10.1111/age.12198. Epub 2014 Jul 18.
SNPQC–an R pipeline for quality control of Illumina SNP genotyping array data.
Gondro C1, Porto-Neto LR, Lee SH.

ArrayMaker 1.1 – Genotyping-by-Sequencing from Aligned Whole Genomes

ArrayMaker 1.1

:: DESCRIPTION

ArrayMaker is a user-friendly tool which extracts accurate single nucleotide polymorphism genotypes at pre-defined loci from whole genome alignments and presents them in a standard genotyping format compatible with association analysis software and datasets genotyped on commercial array platforms.

::DEVELOPER

ArrayMaker team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Perl

:: DOWNLOAD

 ArrayMaker

:: MORE INFORMATION

Citation:

Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker.
Willet CE, Haase B, Charleston MA, Wade CM.
Bioinformatics. 2014 Oct 21. pii: btu691.

GenoTan 0.1.5 – Genotyping of Microsatellite Loci

GenoTan 0.1.5

:: DESCRIPTION

GenoTan is a free tool to identify length variation of microsatellites from short sequence reads. Inferring lengths of inherited microsatellite alleles with single base pair resolution from short sequence reads is challenging due to several sources of noise including PCR amplification errors, individual cell mutation, misalignment or mis-mapping caused by the repetitive nature of the microsatellites. We have developed a method using a discretized Gaussian mixture model combined with a rules-based approach to identify inherited variation of microsatellite loci from short sequence reads, which effectively distinguishes length variants from INDEL errors at homopolymers.

::DEVELOPER

GenoTan team

:: SCREENSHOTS

Command

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 GenoTan

 :: MORE INFORMATION

Citation:

Bioinformatics. 2014 Mar 1;30(5):652-9. doi: 10.1093/bioinformatics/btt595. Epub 2013 Oct 17.
Discretized Gaussian mixture for genotyping of microsatellite loci containing homopolymer runs.
Tae H, Kim DY, McCormick J, Settlage RE, Garner HR.

QuASAR – Joint Genotyping & ASE Inference for RNA-seq data

QuASAR

:: DESCRIPTION

QuASAR (Quantitative allele specific analysis of reads) is an R package, that implements a statistical method for: i) genotyping from next-generation sequencing reads, and ii) conducting inference on allelic imbalance at heterozygous sites.

::DEVELOPER

Roger Pique-Regi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 QuASAR

:: MORE INFORMATION

Citation

QuASAR: Quantitative Allele Specific Analysis of Reads.
Harvey CT, Moyerbrailean GA, Davis GO, Wen X, Luca F, Pique-Regi R.
Bioinformatics. 2014 Dec 4. pii: btu802

Genome STRiP 2.00.1529 – Discovering and Genotyping Structural Variations using Sequencing data

Genome STRiP 2.00.1529

:: DESCRIPTION

Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovering and genotyping structural variations using sequencing data. The methods are designed to detect shared variation using data from multiple individuals, but can also process single genomes.

::DEVELOPER

Genome STRiP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java
  • R package

:: DOWNLOAD

  Genome STRiP

:: MORE INFORMATION

Citation

Handsaker RE, Van Doren V, Berman JR, Genovese G, Kashin S, Boettger LM, McCarroll SA
Large multiallelic copy number variations in humans
Nature Genetics (2015) doi:10.1038/ng.3200

Handsaker RE, Korn JM, Nemesh J, McCarroll SA
Discovery and genotyping of genome structural polymorphism by sequencing on a population scale.
Nature genetics 43, 269-276 (2011)