metaSNV v2.0.1 – Metagenomic SNV Calling Pipeline

metaSNV v2.0.1

:: DESCRIPTION

MetaSNV is a pipeline for calling metagenomic single nucleotide variants (SNVs). It was designed to scale well with the exponentially increasing amount of available metagenomic datasets and is capable of handling large multi-species references.

::DEVELOPER

metaSNV team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

metaSNV

:: MORE INFORMATION

Citation:

Van Rossum T, Costea PI, Paoli L, Alves R, Thielemann R, Sunagawa S, Bork P.
metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes.
Bioinformatics. 2021 Nov 17:btab789. doi: 10.1093/bioinformatics/btab789. Epub ahead of print. PMID: 34791031.

JACUSA v2.0.2-RC – JAVA framework for accurate SNV Assessment

JACUSA v2.0.2-RC

:: DESCRIPTION

JACUSA2 is a one-stop solution to detect single nucleotide variants (SNVs) and reverse transcriptase induced arrest events in Next-generation sequencing (NGS) data.

::DEVELOPER

Dieterich lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Jav

:: DOWNLOAD

JACUSA2

:: MORE INFORMATION

Citation.

Piechotta M, Wyler E, Ohler U, Landthaler M, Dieterich C.
JACUSA: site-specific identification of RNA editing events from replicate sequencing data.
BMC Bioinformatics. 2017 Jan 3;18(1):7. doi: 10.1186/s12859-016-1432-8. PMID: 28049429; PMCID: PMC5210316.

MultiGeMS 1.0 – Detection of SNVs from Multiple Samples Using Model Selection on High-Throughput Sequencing Data

MultiGeMS 1.0

:: DESCRIPTION

MultiGeMS (Multi-sample Genotype Model Selection) is a multiple sample single nucleotide variant (SNV) caller that works with alignment files of high-throughput sequencing (HTS) data. MultiGeMS calls SNVs based on a statistical model selection procedure and accounts for enzymatic substitution sequencing errors.

::DEVELOPER

Cui Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 MultiGeMS

:: MORE INFORMATION

Citation

MultiGeMS: Detection of SNVs from Multiple Samples Using Model Selection on High-Throughput Sequencing Data.
Murillo G, You N, Su X, Cui W, Reilly MP, Li M, Ning K, Cui X.
Bioinformatics. 2016 Jan 18. pii: btv753

PASsiT 1.0 – Post Alignment SNV Tools

PASsiT 1.0

:: DESCRIPTION

PASsiT (Post Alignment SNV Tools) is a suite of tools developed to help in our high-throughput sequencing and analysis environment.With single nucleotide variations (SNVs) being identified in ever increasing numbers with next generation sequencing data, we are often interested in a breakdown of the effect of the mutations, and if a particular change is somatic or germline. We are also interested in high quality true positive mutations, which are increasingly important considering their use in clinical decisions.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PASsiT

:: MORE INFORMATION

See poster presented at RECOMB 2011 for more details:
http://www.bcgsc.ca/downloads/passit/PASsiT.pdf

NGSanalyzer 1.0 – Identifying SNV and Indels from Short Read Sequence data

NGSanalyzer 1.0

:: DESCRIPTION

NGSanalyzer is a suit of tools for identifying SNV (single nucleotide variations) and indels (insertions and deletions) from short read sequence data.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 NGSanalyzer

:: MORE INFORMATION

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