Tag: Caller

ROVER 2.0.0 / UNDR ROVER 2.0.0 – Read Overlap Variant Caller

ROVER 2.0.0 / UNDR ROVER 2.0.0

:: DESCRIPTION

ROVER is a read-pair overlap considerate variant-calling software for PCR-based massively parallel sequencing datasets

UNDR ROVER (Unmapped Primer directed read overlap Variant caller) is an improved version of our ROVER variant calling tool for targeted DNA sequencing.

::DEVELOPER

Bernie Pope

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

 ROVER , UNDR ROVER

:: MORE INFORMATION

Citation:

UNDR ROVER – a fast and accurate variant caller for targeted DNA sequencing.
Park DJ, Li R, Lau E, Georgeson P, Nguyen-Dumont T, Pope BJ.
BMC Bioinformatics. 2016 Apr 16;17(1):165. doi: 10.1186/s12859-016-1014-9.

ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets.
Pope BJ, Nguyen-Dumont T, Hammet F, Park DJ.
Source Code Biol Med. 2014 Jan 24;9(1):3. doi: 10.1186/1751-0473-9-3.

HadoopCNV – MapReduce-based Copy Number Variation Caller for Genome Sequencing data

HadoopCNV

:: DESCRIPTION

HadoopCNV (internal codename: PennCNV3) is a Java implementation of MapReduce-based copy number variation caller for next-generation whole-genome sequencing data.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows with Cygwin/ Linux / MacOSX
  • Perl
  • Java

:: DOWNLOAD

HadoopCNV

:: MORE INFORMATION

Citation

Yang H, Chen G, Lima L, Fang H, Jimenez L, Li M, Lyon GJ, He M, Wang K:
HadoopCNV: A dynamic programming imputation algorithm to detect copy number variants from sequencing data.
bioRxiv, 2017.

SoloDel 1.0.0 – Somatic Low-frequent Deletion Caller Model

SoloDel 1.0.0

:: DESCRIPTION

SoloDel is a Java based somatic deletion caller designed for whole-genome sequencing data from unmatched samples. SoloDel is specialized for identifying somatic deletions with frequently existing sampling issues : low mutational frequency in cell population and absence of the matched control samples.

::DEVELOPER

SoloDel team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 SoloDel

:: MORE INFORMATION

Citation

SoloDel: A probabilistic model for detecting low-frequent somatic deletions from unmatched sequencing data.
Kim J, Kim S, Nam H, Kim S, Lee D.
Bioinformatics. 2015 Jun 11. pii: btv358.

ConsensusFixer 0.4 – Consensus Sequence Caller with Ambiguous bases and in-frame Insertions

ConsensusFixer 0.4

:: DESCRIPTION

ConsensusFixer is a java command line application which computes a consensus sequence with in-frame insertions and ambiguous nucleotide (wobbles) from ultra deep next-generation sequencing alignments.

::DEVELOPER

Armin Töpfer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Java

:: DOWNLOAD

 ConsensusFixer

:: MORE INFORMATION

MetaSV 0.5.4 – Structural-Variant caller for Next Generation Sequencing

MetaSV 0.5.4

:: DESCRIPTION

MetaSVM is an accurate method-aware merging algorithm for structural variations

::DEVELOPER

Roche Sequencing Solutions

:: SCREENSHOTS

N/a

:: REQUIREMENTS

:: DOWNLOAD

 MetaSV

:: MORE INFORMATION

Citation

MetaSV: An accurate and integrative structural-variant caller for next generation sequencing.
Mohiyuddin M, Mu JC, Li J, Asadi NB, Gerstein MB, Abyzov A, Wong WH, Lam HY.
Bioinformatics. 2015 Apr 10. pii: btv204.

Sniffles 1.0.11 – Structural Variation Caller using Third Generation Sequencing

Sniffles 1.0.11

:: DESCRIPTION

Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis.

::DEVELOPER

Sniffles team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Sniffles

:: MORE INFORMATION

Citation

Accurate detection of complex structural variations using single-molecule sequencing.
Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, von Haeseler A, Schatz MC.
Nat Methods. 2018 Jun;15(6):461-468. doi: 10.1038/s41592-018-0001-7.

Bis-SNP 0.82.2 – Bisulfite Space Genotyper & Methylation Caller

BisSNP 0.82.2

:: DESCRIPTION

BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq, RRBS and any other bisulfite treated sequencing) with Illumina directional library protocol.

::DEVELOPER

USC Epigenome Center

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • java
  • perl 

:: DOWNLOAD

 Bis-SNP

:: MORE INFORMATION

Citation

Genome Biol. 2012 Jul 11;13(7):R61. [Epub ahead of print]
Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data.
Liu Y, Siegmund KD, Laird PW, Berman BP.