FlowgramFixer beta – Model the Ion Torrent Sequencing process

FlowgramFixer beta

:: DESCRIPTION

FlowgramFixer is an improved basecaller for the IonTorrent sequencing platform, which reduces error rates, and generates more uniquely aligned reads and more high quality reads than the default base calling algorithm implemented by IonTorrent in TorrentSuite.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows / MacOsX
C Compiler

:: DOWNLOAD

FlowgramFixer

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Jul 1;29(13):i344-51. doi: 10.1093/bioinformatics/btt212.
Using state machines to model the Ion Torrent sequencing process and to improve read error rates.
Golan D1, Medvedev P.

SnackVar v2.4.3 – Sanger Sequencing analysis in Clinical Environment

SnackVar v2.4.3

:: DESCRIPTION

SnackVar is a free software for Sanger sequencing analysis in clinical environment.It supports automatic detection of variants including SNVs and indel variants (homozygous and heterozygous).

::DEVELOPER

Young-gon Kim.

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOS
Java

:: DOWNLOAD

SnackVar

:: MORE INFORMATION

Citation

Kim YG, Kim MJ, Lee JS, Lee JA, Song JY, Cho SI, Park SS, Seong MW.
SnackVar: An Open-Source Software for Sanger Sequencing Analysis Optimized for Clinical Use.
J Mol Diagn. 2021 Feb;23(2):140-148. doi: 10.1016/j.jmoldx.2020.11.001. Epub 2020 Nov 24. PMID: 33246077.

StoatyDive v1.1.0 – Evaluation and Classification of Peak Profiles for Sequencing data

StoatyDive v1.1.0

:: DESCRIPTION

StoatyDive is a tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets. It can be used for sequencing data such as CLIP-seq or ChIP-Seq, or any other type of peak profile data.

::DEVELOPER

Bioinformatics Group Albert-Ludwigs-University Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

StoatyDive

:: MORE INFORMATION

Citation

Heyl F, Backofen R.
StoatyDive: Evaluation and classification of peak profiles for sequencing data.
Gigascience. 2021 Jun 18;10(6):giab045. doi: 10.1093/gigascience/giab045. PMID: 34143874; PMCID: PMC8212874.

G4ALL 1.1 – Graphic Contig Analyzer for All Sequencing Platforms

G4ALL 1.1

:: DESCRIPTION

G4ALL is a stand-alone tool that facilitates the editing of the contigs generated by assembly process. G4ALL use mapping results produced by Blast or Mummer against a reference genome to generate a scaffold based on the overlap of the contigs after curation. Besides providing information on the gene products contained in each contig, obtained through a search of the available biological databases which can be inserted in G4ALL database.

::DEVELOPER

Dr. Rommel Ramos – rommelramos@ufpa.br

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux/MacOsX
Java

:: DOWNLOAD

G4ALL

:: MORE INFORMATION

Citation

Bioinformation. 2013 Jun 29;9(11):599-604. doi: 10.6026/97320630009599. Print 2013.
Graphical contig analyzer for all sequencing platforms (G4ALL): a new stand-alone tool for finishing and draft generation of bacterial genomes.
Ramos RT1, Carneiro AR, Caracciolo PH, Azevedo V, Schneider MP, Barh D, Silva A.

deepEA – Interactive Analysis of Epitranscriptome Sequencing data

deepEA

:: DESCRIPTION

deepEA is a convenient, freely available, web-based platform that is capable to support deep analysis of epitranscriptome sequencing data with several general and specific functionalities.

::DEVELOPER

Ma Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

deepEA

:: MORE INFORMATION

Citation

Zhai J, Song J, Zhang T, Xie S, Ma C.
deepEA: a containerized web server for interactive analysis of epitranscriptome sequencing data.
Plant Physiol. 2021 Feb 25;185(1):29-33. doi: 10.1093/plphys/kiaa008. PMID: 33631802; PMCID: PMC8133649.

NanoMethViz 1.2.0 – Visualise Methlation data from Oxford Nanopore Sequencing

NanoMethViz 1.2.0

:: DESCRIPTION

NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing. It can be used to explore methylation patterns from reads derived from Oxford Nanopore direct DNA sequencing with methylation called by callers including nanopolish, f5c and megalodon.

::DEVELOPER

Shian Su

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
R package / BioConductor

:: DOWNLOAD

NanoMethViz

:: MORE INFORMATION

Citation

Su S, Gouil Q, Blewitt ME, Cook D, Hickey PF, Ritchie ME.
NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data.
PLoS Comput Biol. 2021 Oct 25;17(10):e1009524. doi: 10.1371/journal.pcbi.1009524. Epub ahead of print. PMID: 34695109.

TERA-Seq – True end-to-end Sequencing of native RNA molecules for Transcriptome Characterization

TERA-Seq

:: DESCRIPTION

TERA-Seq (True End-to-end RNA Sequencing) is a platform that addresses these limitations, permitting more thorough transcriptome characterization.

::DEVELOPER

Z. MOURELATOS LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

TERA-Seq

:: MORE INFORMATION

Citation

Ibrahim F, Oppelt J, Maragkakis M, Mourelatos Z.
TERA-Seq: true end-to-end sequencing of native RNA molecules for transcriptome characterization.
Nucleic Acids Res. 2021 Aug 24:gkab713. doi: 10.1093/nar/gkab713. Epub ahead of print. PMID: 34428294.

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

:: 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.