MultiBreak-SV – Detect Structural Variants from Single Molecule Sequencing data

MultiBreak-SV

: DESCRIPTION

MultiBreak-SV is a software for structural variation analysis from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 MultiBreak-SV

:: MORE INFORMATION

Citation:

Characterization of Structural Variants with Single Molecule and Hybrid Sequencing Approaches.
Ritz A, Bashir A, Sindi S, Hsu D, Hajirasouliha I, Raphael BJ.
Bioinformatics. 2014 Oct 28. pii: btu714.

ngs-bits 2021_03 – Short-read sequencing tools

ngs-bits 2021_03

:: DESCRIPTION

ngs-bits is a collection of tools for short-read data analysis.

::DEVELOPER

Arbeitsgruppe Genomik

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Bioconda

:: DOWNLOAD

ngs-bits

:: MORE INFORMATION

Citation

Schroeder CM, Hilke FJ, Löffler MW, Bitzer M, Lenz F, Sturm M.
A comprehensive quality control workflow for paired tumor-normal NGS experiments.
Bioinformatics. 2017 Jun 1;33(11):1721-1722. doi: 10.1093/bioinformatics/btx032. PMID: 28130233.

GBStools – Bioinformatics tools for Reduced Representation Sequencing data

GBStools

:: DESCRIPTION

GBStools provides bioinformatics tools for genotyping-by-sequencing data, including allele frequency estimation at variant restriction sites.

:: DEVELOPER

the Bustamante Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

GBStools

:: MORE INFORMATION

Citation

Cooke TF, Yee MC, Muzzio M, Sockell A, Bell R, Cornejo OE, Kelley JL, Bailliet G, Bravi CM, Bustamante CD, Kenny EE.
GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data.
PLoS Genet. 2016 Feb 1;12(2):e1005631. doi: 10.1371/journal.pgen.1005631. PMID: 26828719; PMCID: PMC4734769.

ODS – Online Diagnosis System for Sanger Sequencing based Genetic Testing

ODS

:: DESCRIPTION

ODS (Online Diagnosis System) is a webserver for analysis of Sanger sequencing-based genetic testing data.

::DEVELOPER

Dr. Sun Hao’s Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Online Diagnosis System: A webserver for analysis of Sanger sequencing-based genetic testing data.
Sun K, Yuen YP, Wang H, Sun H.
Methods. 2014 Jul 22. pii: S1046-2023(14)00239-4. doi: 10.1016/j.ymeth.2014.07.002.

SToRM 0.0099 – Seed-based Read Mapping tool for SOLiD or Illumina sequencing data

SToRM 0.0099

:: DESCRIPTION

SToRM is a software tool primarily proposed for mapping SOLiD reads or Illumina reads to a reference genome. It was based on seeding techniques adapted to the statistical characteristics of the reads: the default seeds are for example designed (using the Iedera software) to comply with the properties of the SOLiD color encoding, or Illumina more classical encoding as well as the observed reading error distribution along the read.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux / MacOsX
  • C Compiler

:: DOWNLOAD

 SToRM

:: MORE INFORMATION

Citation

Noé, L. and Gîrdea,. and Kucherov, G.:
Designing efficient spaced seeds for SOLiD read mapping
Advances in Bioinformatics, Volume 2010 2010

SRMA 1.0.0-2 – Analyze Array-based Sequencing data for Identifying Rare DNA Variants

SRMA 1.0.0-2

:: DESCRIPTION

SRMA is an R package for resequencing microarray data analysis that integrates a novel statistical algorithm, sequence robust multi-array analysis, for rare variant detection with high sensitivity and accuracy.

::DEVELOPER

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

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX
  • R package

:: DOWNLOAD

  SRMA

:: MORE INFORMATION

Citation

SRMA: an R package for resequencing array data analysis.
Zhang N, Xu Y, O’Hely M, Speed TP, Scharfe C, Wang W.
Bioinformatics. 2012 Jul 15;28(14):1928-30. doi: 10.1093/bioinformatics/bts286

BIMA v3 – Aligner customized for Mate Pair Library Sequencing

BIMA v3

:: DESCRIPTION

BIMA is a mapping/alignment customized for mate-pair library next generation sequencing.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BIMA

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 1;30(11):1627-9. doi: 10.1093/bioinformatics/btu078. Epub 2014 Feb 12.
BIMA V3: an aligner customized for mate pair library sequencing.
Drucker TM, Johnson SH, Murphy SJ, Cradic KW, Therneau TM, Vasmatzis G.

CHIP-RNA-SEQPRO 1.1 – ChIP-RNA-sequencing-processing

CHIP-RNA-SEQPRO 1.1

:: DESCRIPTION

ChIP-RNA-seqPRO: A strategy for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing sites.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R package

:: DOWNLOAD

   CHIP-RNA-SEQPRO

:: MORE INFORMATION

LongGF v0.1.2 – Detection of Gene Fusion by long-read Transcriptome Sequencing

LongGF v0.1.2

:: DESCRIPTION

LongGF is a fast computational tool to efficiently detect candidate gene fusion from long-read RNA-seq data, including cDNA sequencing data and direct mRNA sequencing data.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOSX / Windows
  • C++

:: DOWNLOAD

LongGF

:: MORE INFORMATION

Citation

Liu Q, Hu Y, Stucky A, Fang L, Zhong JF, Wang K.
LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing.
BMC Genomics. 2020 Dec 29;21(Suppl 11):793. doi: 10.1186/s12864-020-07207-4. PMID: 33372596; PMCID: PMC7771079.

BarNone – Match barcodes in Sequencing data based on Levenshtein Distance

BarNone

:: DESCRIPTION

BarNone is a tool for matching and counting sequencing barcodes, such as those produced by barcode sequencing (Bar-Seq), to a catalog.

::DEVELOPER

STOREY LAB | Princeton University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 BarNone

:: MORE INFORMATION