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.

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.

Isaac / isaac_aligner 01.15.04.01 / isaac_variant_caller 1.0.7 – Genome Aligner and Variant Caller

Isaac / isaac_aligner 01.15.04.01 / isaac_variant_caller 1.0.7

:: DESCRIPTION

Isaac is ultra-fast whole-genome secondary analysis on Illumina sequencing platforms. An ultrafast DNA sequence aligner /isaac_aligner (Isaac Genome Alignment Software) that takes advantage of high-memory hardware (>48 GB) and variant caller (isaac_variant_caller– Isaac Variant Caller) have been developed.

::DEVELOPER

Illumina, Inc.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

  Isaac

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 15;29(16):2041-3. doi: 10.1093/bioinformatics/btt314. Epub 2013 Jun 4.
Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms.
Raczy C, Petrovski R, Saunders CT, Chorny I, Kruglyak S, Margulies EH, Chuang HY, Källberg M, Kumar SA, Liao A, Little KM, Strömberg MP, Tanner SW.

VarScan 2.4.0 – Variant Caller for Short Sequence Reads

VarScan 2.4.0

:: DESCRIPTION

VarScan is a platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequencyh. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples.

::DEVELOPER

The Genome Institute at Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

 VarScan

:: MORE INFORMATION

Citation:

Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, & Ding L (2009).
VarScan: variant detection in massively parallel sequencing of individual and pooled samples.
Bioinformatics (Oxford, England), 25 (17), 2283-5 PMID:

bam2mpg 1.0.1 – Bayesian Genotype Caller for NextGen Sequencing Data

bam2mpg 1.0.1

:: DESCRIPTION

bam2mpg calls genotypes from sequence reads of haploid or diploid DNA aligned to a closely-related reference sequence. The program reads alignments in BAM format (http://samtools.sourceforge.net). The MPG (Most Probable Genotype) algorithm is based on a Bayesian model which simulates sampling from one or two alleles with sequencing error, and then calculates the likelihood of each possible genotype given the observed sequence data. Using prior probabilities dependent on the expected heterozygosity of the sequence, MPG then predicts the “Most Probable Genotype” at each site, along with quality scores estimating the accuracy of the calls.

::DEVELOPER

bam2mpg Team  @ NHGRI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 bam2mpg

:: MORE INFORMATION

Manta 0.29.2 – Structural Variant and Indel Caller for Mapped Sequencing data

Manta 0.29.2

:: DESCRIPTION

Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads.

::DEVELOPER

Illumina

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 Manta

:: MORE INFORMATION

Citation

Manta: Rapid detection of structural variants and indels for germline and cancer sequencing applications.
Chen X, Schulz-Trieglaff O, Shaw R, Barnes B, Schlesinger F, K?llberg M, Cox AJ, Kruglyak S, Saunders CT.
Bioinformatics. 2015 Dec 8. pii: btv710

Q v1.1.0 – Saturation-based ChIP-seq Peak Caller

Q v1.1.0

:: DESCRIPTION

Q is a fast saturation-based ChIP-seq peak caller. Q works well in conjunction with the irreproducible discovery rate (IDR) procedure.

::DEVELOPER

The Computational Biology @ Charité Berlin at the Institute for Medical Genetics and Human Genetics at Charité-Universitätsmedizin Berlin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Q

:: MORE INFORMATION

Citation

Genome Res. 2015 Sep;25(9):1391-400. doi: 10.1101/gr.189894.115.
Saturation analysis of ChIP-seq data for reproducible identification of binding peaks.
Hansen P, Hecht J, Ibrahim DM, Krannich A, Truss M, Robinson PN.