Tag: paired-end

SVDetect 0.8b – Detect Genomic Structural Variations from Paired-end and Mate-pair Sequencing data

SVDetect 0.8b

:: DESCRIPTION

SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies.

::DEVELOPER

Boeva lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SVDetect

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Aug 1;26(15):1895-6.
SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data.
Zeitouni B, Boeva V, Janoueix-Lerosey I, Loeillet S, Legoix-né P, Nicolas A, Delattre O, Barillot E.

AscatNGS 4.4.1 – Somatic Copy Number analysis using WGS paired end wholegenome sequencing

AscatNGS 4.4.1

:: DESCRIPTION

AscatNGS contains the Cancer Genome Projects workflow implementation of the ASCAT copy number algorithm for paired end sequencing.

::DEVELOPER

CASM IT

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl

:: DOWNLOAD

AscatNGS

:: MORE INFORMATION

Citation

Raine KM, Van Loo P, Wedge DC, Jones D, Menzies A, Butler AP, Teague JW, Tarpey P, Nik-Zainal S, Campbell PJ.
ascatNgs: Identifying Somatically Acquired Copy-Number Alterations from Whole-Genome Sequencing Data.
Curr Protoc Bioinformatics. 2016 Dec 8;56:15.9.1-15.9.17. doi: 10.1002/cpbi.17. PMID: 27930809; PMCID: PMC6097604.

ABySS 2.3.2 – de novo, parallel, paired-end Sequence Assembler

ABySS 2.3.2

:: DESCRIPTION

ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 ABySS

:: MORE INFORMATION

Citation

Paulino D, Warren RL, Vandervalk BP, Raymond A, Jackman SD, Birol I.
Sealer: a scalable gap-closing application for finishing draft genomes.
BMC Bioinformatics. 2015 Jul 25;16(1):230. doi: 10.1186/s12859-015-0663-4. PMID: 26209068; PMCID: PMC4515008.

Vandervalk BP, Yang C, Xue Z, Raghavan K, Chu J, Mohamadi H, Jackman SD, Chiu R, Warren RL, Birol I.
Konnector v2.0: pseudo-long reads from paired-end sequencing data.
BMC Med Genomics. 2015;8 Suppl 3(Suppl 3):S1. doi: 10.1186/1755-8794-8-S3-S1. Epub 2015 Sep 23. PMID: 26399504; PMCID: PMC4582294.

Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.
ABySS: A parallel assembler for short read sequence data.
Genome Res. 2009. 19: 1117-1123

Circall v0.1.0 – Discovery of Circular RNAs from Paired-end RNA-sequencing data

Circall v0.1.0

:: DESCRIPTION

Circall is a novel method for fast and accurate discovery of circular RNAs from paired-end RNA-sequencing data.

::DEVELOPER

Dat T Nguyen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

Circall

:: MORE INFORMATION

Citation

Nguyen DT, Trac QT, Nguyen TH, Nguyen HN, Ohad N, Pawitan Y, Vu TN.
Circall: fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data.
BMC Bioinformatics. 2021 Oct 13;22(1):495. doi: 10.1186/s12859-021-04418-8. PMID: 34645386; PMCID: PMC8513298.

BreakFusion 1.0.1 – Identify Gene Fusions from paired-end RNA-Seq data

BreakFusion 1.0.1

:: DESCRIPTION

BreakFusion is a software that combines the strength of reference alignment followed by read-pair analysis and de novo assembly to achieve a good balance in sensitivity, specificity and computational efficiency.

::DEVELOPER

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 BreakFusion

:: MORE INFORMATION

Citation:

Ken Chen et al.
BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data
Bioinformatics (2012) 28 (14): 1923-1924.

FuSeq 1.1.4 – Discover Fusion Genes from paired-end RNA Sequencing data

FuSeq 1.1.4

:: DESCRIPTION

FuSeq discovers fusion genes based on quasi-mapping to quickly map the reads, extract initial candidates from split reads and fusion equivalence classes of mapped reads, and finally apply multiple filters and statistical tests to get the final candidates.

::DEVELOPER

PROF. YUDI PAWITAN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

FuSeq

:: MORE INFORMATION

Citation

Vu TN, Deng W, Trac QT, Calza S, Hwang W, Pawitan Y.
A fast detection of fusion genes from paired-end RNA-seq data.
BMC Genomics. 2018 Nov 1;19(1):786. doi: 10.1186/s12864-018-5156-1. PMID: 30382840; PMCID: PMC6211471.

PANDASEQ 2.11 / Pandaseq-sam 1.4 – PAired-eND Assembler for DNA sequences

PANDASEQ 2.11 / Pandaseq-sam 1.4

:: DESCRIPTION

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

PANDASEQ-SAM is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. This version works on SAM/BAM formatted files.

::DEVELOPER

Neufeld Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • C Compiler 

:: DOWNLOAD

 PANDASEQ , PANDASEQ-SAM

:: MORE INFORMATION

Citation

Andre P Masella, Andrea K Bartram, Jakub M Truszkowski, Daniel G Brown and Josh D Neufeld.
PANDAseq: paired-end assembler for illumina sequences.
BMC Bioinformatics 2012, 13:31.

PASSion 1.2.1 – Pattern Growth algorithm based Pileline for Splice Site Detection in Paired-end RNA-Seq data

PASSion 1.2.1

:: DESCRIPTION

PASSion uses the mapped read in a pair as anchor and then uses a high resolution algorithm, pattern growth, to remap the proximal and distal fragments of the unmapped read to a local region of the reference indicated by the mate. It is capable of identifying both known and novel canonical and non-canonical junctions with SNP or sequencing error tolerance.

::DEVELOPER

Yanju Zhang (Leiden University Medical Center, The Netherlands): y.zhang AT lumc.nl

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PASSion

:: MORE INFORMATION

Citation:

PASSion: A Pattern Growth Algorithm Based Pipeline for Splice Junction Detection in Paired-end RNA-Seq Data
Yanju Zhang; Eric-Wubbo Lameijer; Peter A.C. ‘t Hoen; Zemin Ning; P. Eline Slagboom; Kai Ye
Bioinformatics 2012; doi: 10.1093/bioinformatics/btr712

FusionAnalyser – Detect Gene Fusions from paired-end RNA-Seq data

FusionAnalyser

:: DESCRIPTION

FusionAnalyser is a software for detecting gene fusions from paired-end RNA-Seq data.FusionAnalyser uses paired reads mapping to different genes (Bridge reads),  generated through high-throughput whole transcriptome sequencing, to build a first dataset of candidate fusion events. Subsequently, a second dataset, built upon those reads where only one of the two sequences in a pair is successfully mapped to the reference genome (‘Half-mapped Anchor reads’), is generated. The mapped reads in the latter dataset are used as an anchor to tie each Half-mapped event to the corresponding Bridge region.

::DEVELOPER

Rocco Piazza 

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / WIndows

:: DOWNLOAD

 FusionAnalyser 

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Sep 1;40(16):e123. Epub 2012 May 8.
FusionAnalyser: a new graphical, event-driven tool for fusion rearrangements discovery.
Piazza R, Pirola A, Spinelli R, Valletta S, Redaelli S, Magistroni V, Gambacorti-Passerini C.

misFinder v0.4.05.05 – Identify Mis-assemblies in an unbiased manner using Reference and Paired-end Reads

misFinder v0.4.05.05

:: DESCRIPTION

misFinder is a tool that aims to identify the assembly errors with high accuracy in an unbiased way and correct these errors at their mis-assembled positions to improve the assembly accuracy for downstream analysis.

::DEVELOPER

misFinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 misFinder

:: MORE INFORMATION

Citation

misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads.
Zhu X, Leung HC, Wang R, Chin FY, Yiu SM, Quan G, Li Y, Zhang R, Jiang Q, Liu B, Dong Y, Zhou G, Wang Y.
BMC Bioinformatics. 2015 Nov 16;16(1):386.

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