LRSDAY v1.6.0 – Long-read Sequencing Data Analysis for Yeasts

LRSDAY v1.6.0

:: DESCRIPTION

LRSDAY is a highly transparent, automated and powerful computational framework for high-quality genome assembly and annotation.

::DEVELOPER

Jia-Xing Yue

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

LRSDAY

:: MORE INFORMATION

Citation

Yue JX, Liti G.
Long-read sequencing data analysis for yeasts.
Nat Protoc. 2018 Jun;13(6):1213-1231. doi: 10.1038/nprot.2018.025. Epub 2018 May 3. PMID: 29725120.

MiXCR 3.0.13 – Analysis of T- and B- cell Receptor Repertoire Sequencing data

MiXCR 3.0.13

:: DESCRIPTION

MiXCR is an universal software for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data

::DEVELOPER

MiLaboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • JRE
:: DOWNLOAD

 MiXCR

:: MORE INFORMATION

Citation:

Nat Methods. 2015 May;12(5):380-1. doi: 10.1038/nmeth.3364.
MiXCR: software for comprehensive adaptive immunity profiling.
Bolotin DA, Poslavsky S, Mitrophanov I, Shugay M3, Mamedov IZ, Putintseva EV, Chudakov DM.

DNAApp 1.2.7 – Mobile Application for Sequencing Data Analysis

DNAApp 1.2.7

:: DESCRIPTION

The DNAApp opens and allows the analysis of ab1 DNA sequencing files. When used in combination with other apps (zip apps), and also web tools like Blast,ClustalW (accessible from the web browser on your phone), this app allows you to analyse and determine the quality of your sequencing files.

::DEVELOPER

Antibody & Product Development Team of BII-p53Lab ASTAR

:: SCREENSHOTS

DNAApp

:: REQUIREMENTS

  • iOS / Android

:: DOWNLOAD

 DNAApp for iOS / for Android

:: MORE INFORMATION

Citation

DNAApp: a mobile application for sequencing data analysis.
Nguyen PV, Verma CS, Gan SK.
Bioinformatics. 2014 Aug 5. pii: btu525.

FLAM-seq 1.0.0 – Full-length poly(A) and mRNA Sequencing

FLAM-seq 1.0.0

:: DESCRIPTION

FLAM-seq is a rapid and simple method for high-quality sequencing of entire mRNAs.

::DEVELOPER

N. Rajewsky Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

FLAM-seq

:: MORE INFORMATION

Citation

Legnini I, Alles J, Karaiskos N, Ayoub S, Rajewsky N.
FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control.
Nat Methods. 2019 Sep;16(9):879-886. doi: 10.1038/s41592-019-0503-y. Epub 2019 Aug 5. PMID: 31384046.

FunctionSIM – A Sequencing Simulator for Functional Metagenomics

FunctionSIM

:: DESCRIPTION

FunctionSIM is a bioinformatics tool to generate microbial DNA sequences. As standalone software it allows users to simulate metagenomic sequence datasets that can be used as standardized test data for planning metagenomic projects or for benchmarking software in functional metagenomic analysis.

::DEVELOPER

Lingling An

:: SCREENSHOTS

FunctionSIM

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 FunctionSIM

:: MORE INFORMATION

ArrayMaker 1.1 – Genotyping-by-Sequencing from Aligned Whole Genomes

ArrayMaker 1.1

:: DESCRIPTION

ArrayMaker is a user-friendly tool which extracts accurate single nucleotide polymorphism genotypes at pre-defined loci from whole genome alignments and presents them in a standard genotyping format compatible with association analysis software and datasets genotyped on commercial array platforms.

::DEVELOPER

ArrayMaker team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Perl

:: DOWNLOAD

 ArrayMaker

:: MORE INFORMATION

Citation:

Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker.
Willet CE, Haase B, Charleston MA, Wade CM.
Bioinformatics. 2014 Oct 21. pii: btu691.

GenoMS 20120110 – Sequencing Whole Proteins using a Template Databases

GenoMS 20120110

:: DESCRIPTION

GenoMS is a tool for sequencing a small set of proteins using an imperfect database and tandem mass spectra. The database need not contain full protein sequence, but instead can contain exons or partial sequences. The database can also be a small region of the genome. Tandem mass spectra should be from overlapping peptides produced from digestion by multiple proteases.

::DEVELOPER

Natalie Castellana  ,CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

   GenoMS

:: MORE INFORMATION

Citation:

Template Proteogenomics: sequencing whole proteins using an imperfect database.
NE Castellana, V Pham, D Arnott, JR Lill, V Bafna. (2010).
Mol. Cell. Proteomics, 9, 6:1260-70.

QPLOT 20130627 – Quality Assessment and Diagnosis tool for Sequencing

QPLOT 20130627

:: DESCRIPTION

QPLOT calculates various summary statistics some of which are plotted in a PDF file. These statistics can be used to assess the sequencing quality of sequence reads and include empirical base quality scores, GC biases, insert size distribution, depth distribution, genome coverage, empirical Q20 count, and so on.

::DEVELOPER

QPLOT team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 QPLOT

:: MORE INFORMATION

Citation

Bingshan Li, Xiaowei Zhan, Mary-Kate Wing, Paul Anderson, Hyun Min Kang, and Goncalo R. Abecasis,
QPLOT: A Quality Assessment Tool for Next Generation Sequencing Data,”
BioMed Research International, vol. 2013, Article ID 865181, 4 pages, 2013. doi:10.1155/2013/865181

Genome STRiP 2.00.1529 – Discovering and Genotyping Structural Variations using Sequencing data

Genome STRiP 2.00.1529

:: DESCRIPTION

Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovering and genotyping structural variations using sequencing data. The methods are designed to detect shared variation using data from multiple individuals, but can also process single genomes.

::DEVELOPER

Genome STRiP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java
  • R package

:: DOWNLOAD

  Genome STRiP

:: MORE INFORMATION

Citation

Handsaker RE, Van Doren V, Berman JR, Genovese G, Kashin S, Boettger LM, McCarroll SA
Large multiallelic copy number variations in humans
Nature Genetics (2015) doi:10.1038/ng.3200

Handsaker RE, Korn JM, Nemesh J, McCarroll SA
Discovery and genotyping of genome structural polymorphism by sequencing on a population scale.
Nature genetics 43, 269-276 (2011)

BStools – Bisulfite Sequencing Tools

BStools

:: DESCRIPTION

BStools is a sequential trimming-and-retrieving alignment approach for investigating DNA methylation patterns, which significantly improves the number of mapped reads and covered CpG sites.

::DEVELOPER

BStools team

:: SCREENSHOTS

N/a

::REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Perl

:: DOWNLOAD

 BStools

:: MORE INFORMATION

Citation

A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing.
Wang X, Yu X, Zhu W, McCombie WR, Antoniou E, Powers RS, Davidson NO, Li E, Williams J.
Bioinformatics. 2015 Feb 13. pii: btv089