MentaLiST v0.2.5 – A fast MLST caller for large MLST schemes

MentaLiST v0.2.5

:: DESCRIPTION

MLST (multi-locus Sequence Typing) is a classic technique for genotyping bacteria, widely applied for pathogen outbreak surveillance.

MentaLiST is a new MLST caller, based on a k-mer counting algorithm and written in the Julia language, specifically designed and implemented to handle large typing schemes.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python
conda

:: DOWNLOAD

MentaLiST

:: MORE INFORMATION

Citation

Feijao P, Yao HT, Fornika D, Gardy J, Hsiao W, Chauve C, Chindelevitch L.
MentaLiST – A fast MLST caller for large MLST schemes.
Microb Genom. 2018 Feb;4(2):e000146. doi: 10.1099/mgen.0.000146. Epub 2018 Jan 10. PMID: 29319471; PMCID: PMC5857373.

HapMuC 1.0 – Somatic Mutation Caller

HapMuC 1.0

:: DESCRIPTION

HapMuC is a somatic mutation caller, which can utilize the information of heterozygous germline variants near candidate mutations.

::DEVELOPER

Naoto Usuyama

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
GCC
Boost
SAMtools
BEDTools

:: DOWNLOAD

HapMuC

:: MORE INFORMATION

Citation

HapMuC: somatic mutation calling using heterozygous germline variants near candidate mutations.
Usuyama N, Shiraishi Y, Sato Y, Kume H, Homma Y, Ogawa S, Miyano S, Imoto S.
Bioinformatics. 2014 Aug 14. pii: btu537

BreakDancer 1.4.5 – Structural Variation Caller for Paired-end Data

BreakDancer 1.4.5

:: DESCRIPTION

BreakDancer is a package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads.

::DEVELOPER

Ding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ WIndows/MacOsX
Perl/C++

:: DOWNLOAD

BreakDancer

:: MORE INFORMATION

Citation:

Ken Chen, John W Wallis, Michael D McLellan, David E Larson, Joelle M Kalicki, Craig S Pohl, Sean D McGrath, Michael C Wendl, Qunyuan Zhang2, Devin P Locke, Xiaoqi Shi, Robert S Fulton, Timothy J Ley, Richard K Wilson, Li Ding1 & Elaine R Mardis1
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation
Nature Methods 6, 677 – 681 (2009)

Q v1.2.0 – Saturation-based ChIP-seq Peak Caller

Q v1.2.0

:: 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

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

:: 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.

Manta 1.6.0 – Structural Variant and Indel Caller for Mapped Sequencing data

Manta 1.6.0

:: 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

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

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 McDonnell Genome Institute (MGI) 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:

BayClone / BayClone2 1.1 – A Bayesian Sequence and Copy Number Caller for Subclones Using NGS Data

BayClone / BayClone2 1.1

:: DESCRIPTION

BayClone2 as an extension of BayClone provides a Bayesian solution using next-generation sequencing (NGS) data for joint inference on both, structure and sequencing variants within a subclone.

::DEVELOPER

Yuan Ji Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
R

:: DOWNLOAD

BayClone / BayClone2

:: MORE INFORMATION

Citation

Pac Symp Biocomput. 2015;20:467-78.
Bayclone: bayesian nonparametric inference of tumor subclones using ngs data.
Sengupta S1, Wang J, Lee J, Müller P, Gulukota K, Banerjee A, Ji Y.

Bayesian Inference for Tumor Subclones Accounting for Sequencing and Structural Variants
Juhee Lee, Peter Mueller, Subhajit Sengupta, Kamalakar Gulukota, Yuan Ji
arXiv:1409.7158 [stat.ME]

MuSE 1.0-RC – Somatic Point Mutation Caller

MuSE 1.0-RC

:: DESCRIPTION

MuSE (Mutation calling using a Markov Substitution model for Evolution) is a novel approach for modeling the evolution of the allelic composition of the tumor and normal tissue at each reference base.

::DEVELOPER

Statistical Bioinformatics Lab, The University of Texas M. D. Anderson Cancer Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux /MacOsX/Windows
C++ Compiler

:: DOWNLOAD

MuSE

:: MORE INFORMATION

Citation

Fan Y, Xi L, Hughes DS, Zhang J, Zhang J, Futreal PA, Wheeler DA, Wang W.
MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data.
Genome Biol. 2016 Aug 24;17(1):178. doi: 10.1186/s13059-016-1029-6. PMID: 27557938; PMCID: PMC4995747.