Tag: Next-generation Sequencing Data

SRinversion – Detection of Short Inversions in Human Genome using Next Generation Sequencing Data

SRinversion

:: DESCRIPTION

SRinversion is a framework to analyze poorly mapped or unmapped reads by splitting and re-aligning them for the purpose of inversion detection.

::DEVELOPER

WANLING YANG’S GROUP IN BIOINFORMATICS @ University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
  • Perl

:: DOWNLOAD

 SRinversion

:: MORE INFORMATION

Citation

SRinversion: a tool for detecting short inversions by splitting and re-aligning poorly mapped and unmapped sequencing reads.
Chen R, Lau YL, Zhang Y, Yang W.
Bioinformatics. 2016 Aug 8. pii: btw516

HLAreporter 1.03 – HLA Typing from Next Generation Sequencing data

HLAreporter 1.03

:: DESCRIPTION

HLAreporter (HLA reporter) is a novel tool  for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles, followed by de novo assembly of the gene-specific short reads.

::DEVELOPER

WANLING YANG’S GROUP IN BIOINFORMATICS @ University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 HLAreporter

:: MORE INFORMATION

Citation

HLAreporter: a tool for HLA typing from next generation sequencing data.
Huang Y, Yang J, Ying D, Zhang Y, Shotelersuk V, Hirankarn N, Sham PC, Lau YL, Yang W.
Genome Med. 2015 Mar 16;7(1):25. doi: 10.1186/s13073-015-0145-3.

ngsTools 1.0.2 – Population Genetics Analyses from Next-generation Sequencing data

ngsTools 1.0.2

:: DESCRIPTION

ngsTools is a collection of programs for population genetics analyses from NGS data, taking into account data statistical uncertainty.

::DEVELOPER

ngsTools team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

ngsTools

:: MORE INFORMATION

Citation

ngsTools: methods for population genetics analyses from next-generation sequencing data.
Fumagalli M, Vieira FG, Linderoth T, Nielsen R.
Bioinformatics. 2014 May 15;30(10):1486-7. doi: 10.1093/bioinformatics/btu041.

Knime4Bio – Custom Nodes for the Interpretation of Next Generation Sequencing data with KNIME

Knime4Bio

:: DESCRIPTION

Knime4Bio is a set of custom nodes for the KNIME (The Konstanz Information Miner) graphical workbench, for analysing NGS data without the requirement of programming skills.

::DEVELOPER

Knime4Bio team

:: SCREENSHOTS

Knime4Bio

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • KNIME

:: DOWNLOAD

 Knime4Bio

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Nov 15;27(22):3200-1. doi: 10.1093/bioinformatics/btr554. Epub 2011 Oct 7.
Knime4Bio: a set of custom nodes for the interpretation of next-generation sequencing data with KNIME.
Lindenbaum P, Le Scouarnec S, Portero V, Redon R.

RetroSeq 1.41 – Transposable Element Discovery from Next-generation sequencing data

RetroSeq 1.41

:: DESCRIPTION

RetroSeq is a tool for discovery and genotyping of transposable element variants (TEVs) (also known as mobile element insertions) from next-gen sequencing reads aligned to a reference genome in BAM format. The goal is to call TEVs that are not present in the reference genome but present in the sample that has been sequenced. It should be noted that RetroSeq can be used to locate any class of viral insertion in any species where whole-genome sequencing data with a suitable reference genome is available.

::DEVELOPER

Genomics & Genetics At The Sanger Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 RetroSeq

:: MORE INFORMATION

Citation

RetroSeq: transposable element discovery from next-generation sequencing data
Thomas M. Keane, Kim Wong and David J. Adams
Bioinformatics (2013) 29 (3): 389-390.

ZOOM 1.5 – Next Generation Sequencing Data Mapping and Visualization

ZOOM 1.5

:: DESCRIPTION

ZOOM (Zillions Of Oligos Mapped) is a next generation sequencing data mapping and visualization software. Using ZOOM, zillions of short reads are mapped back to reference genomes, including post-analysis at unparalleled in speed, at full sensitivity.1 Throughout the next few pages, ZOOM’s features, capabilities, even benchmarking will be presented, to provide researchers with as much information about the software as possible.

::DEVELOPER

Bioinformatics Solutions Inc

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 ZOOM

:: MORE INFORMATION

Citation:

Lin H, Zhang Z, Zhang MQ, Ma B, Li M.
ZOOM! Zillions Of Oligos Mapped.
Bioinformatics. 2008 Nov 1;24(21):2431-7.