KisSplice 2.4.0-p1 – Local Transcriptome Assembler for SNPs and AS events

KisSplice 2.4.0-p1

:: DESCRIPTION

KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler, which enables to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number of biological conditions, and will quantify each variant in each condition. It has been tested on Illumina datasets of up to 300M reads.

::DEVELOPER

KisSplice Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac OS X /  Linux

:: DOWNLOAD

 KisSplice

:: MORE INFORMATION

Citation

Gustavo AT Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo and Vincent Lacroix,
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.
BMC Bioinformatics 2012, 13(Suppl 6):S5

SATRAP 0.2 – SOLiD Assembler TRAnslation Program

SATRAP 0.2

:: DESCRIPTION

SATRAP is a computer program designed to efficiently translate de novo assembled color-space sequences into a base-space format.

::DEVELOPER

CRIBI Biotechnology Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SATRAP

:: MORE INFORMATION

Citation

SATRAP: SOLiD Assembler TRAnslation Program.
Campagna D, Gasparini F, Franchi N, Manni L, Telatin A, Vitulo N, Ballarin L, Valle G.
PLoS One. 2015 Sep 14;10(9):e0137436. doi: 10.1371/journal.pone.0137436.

IVA 1.0.3 – Iterative Virus Assembler

IVA 1.0.3

:: DESCRIPTION

IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high and variable depth.

::DEVELOPER

The Pathogen genomics team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 IVA

:: MORE INFORMATION

Citation

IVA: accurate de novo assembly of RNA virus genomes.
Hunt M, Gall A, Ong SH, Brener J, Ferns B, Goulder P, Nastouli E, Keane JA, Kellam P, Otto TD.
Bioinformatics. 2015 Feb 28. pii: btv120.

SFA-SPA 0.2.1 – A Suffix Array based Short Peptide Assembler for Metagenomic Data

SFA-SPA 0.2.1

:: DESCRIPTION

SFA-SPA is a suffix array based short peptide assembler for metagenomic data

::DEVELOPER

SFA-SPA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 SFA-SPA

:: MORE INFORMATION

Citation

SFA-SPA: a suffix array based short peptide assembler for metagenomic data.
Yang Y, Zhong C, Yooseph S.
Bioinformatics. 2015 Jan 30. pii: btv052.

Celera Assembler 8.3 – Whole Genome Shotgun Assembler

Celera Assembler 8.3

:: DESCRIPTION

Celera Assembler (wgs-assembler) is scientific software for DNA research. It can reconstruct long sequences of genomic DNA given the fragmentary data produced by whole-genome shotgun sequencing. The Celera Assembler has enabled discovery in microbial genomes, large eukaryotic genomes, diploid genomes, and genomes from environmental samples. Celera Assembler contributed the first diploid sequence of an individual human, and metagenomics assemblies of the Global Ocean Sampling

::DEVELOPER

Celera Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Celera Assembler

:: MORE INFORMATION

Citation

Denisov et al. (2008)
Consensus Generation and Variant Detection by Celera Assembler.
Bioinformatics 24(8):1035-40

Minia 2.0.3 – Short-read Assembler based on a de Bruijn graph

Minia 2.0.3

:: DESCRIPTION

Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day

::DEVELOPER

Rayan Chikhi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Minia

:: MORE INFORMATION

Citation

R. Chikhi, G. Rizk.
Space-efficient and exact de Bruijn graph representation based on a Bloom filter,
WABI 2012

MaSuRCA 3.1.3 – Whole Genome Short Read Assembler

MaSuRCA 3.1.3

:: DESCRIPTION

MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454).

::DEVELOPER

IPST GENOME ASSEMBLY GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MaSuRCA

:: MORE INFORMATION

Citation

The MaSuRCA genome assembler.
Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA.
Bioinformatics. 2013 Nov 1;29(21):2669-77. doi: 10.1093/bioinformatics/btt476.

StriDe – novel Assembler

StriDe

:: DESCRIPTION

The StriDe Assembler integrates string and de Bruijn graph by decomposing reads within error-prone regions, while extending paire-end read into long reads for assembly through repetitive regions.

::DEVELOPER

Huang YT ythuang@cs.ccu.edu.tw.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

StriDe

:: MORE INFORMATION

Citation

Integration of String and de Bruijn Graphs for Genome Assembly.
Huang YT, Liao CF.
Bioinformatics. 2016 Jan 10. pii: btw011.

SGA 0.10.14 – String Graph Assembler

SGA 0.10.14

:: DESCRIPTION

SGA is a de novo assembler designed to assemble large genomes from high coverage short read data. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.

::DEVELOPER

Jared Simpson , Richard Durbin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SGA

:: MORE INFORMATION

Citation

Genome Res. 2012 Mar;22(3):549-56. doi: 10.1101/gr.126953.111.
Efficient de novo assembly of large genomes using compressed data structures.
Simpson JT, Durbin R.

PEAR 0.9.6 – Pair-End reads AssembleR

PEAR 0.9.6

:: DESCRIPTION

PEAR is an ultrafast, memory-efficient and highly accurate pair-end reads assembler. It is fully parallelized and can run with as low as just a few kilobytes of memory.

::DEVELOPER

The Exelixis Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PEAR

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 1;30(5):614-20. doi: 10.1093/bioinformatics/btt5
PEAR: A fast and accurate Illumina Paired-End reAd mergeR.
Zhang J, Kobert K, Flouri T, Stamatakis A.