ShoRAH v1.9.95 – Short Reads Assembly into Haplotypes

ShoRAH v1.9.95

:: DESCRIPTION

ShoRAH is a software package that allows for inference about the structure of a population from a set of short sequence reads as obtained from ultra-deep sequencing of a mixed sample. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ShoRAH

:: MORE INFORMATION

Citation

Zagordi O, Bhattacharya A, Eriksson N, Beerenwinkel N (2011)
ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.
BMC Bioinformatics, vol. 12 p. 119

HaploClique 1.3.1 – Viral Quasispecies Assembly from Paired-end data

HaploClique 1.3.1

:: DESCRIPTION

HaploClique is a computational approach to reconstruct the structure of a viral quasispecies from next-generation sequencing data as obtained from bulk sequencing of mixed virus samples.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 HaploClique

:: MORE INFORMATION

Citation:

Viral quasispecies assembly via maximal clique enumeration.
Töpfer A, Marschall T, Bull RA, Luciani F, Schönhuth A, Beerenwinkel N.
PLoS Comput Biol. 2014 Mar 27;10(3):e1003515. doi: 10.1371/journal.pcbi.1003515.

MetaProb v2 – Accurate Metagenomic Reads Binning based on Probabilistic Sequence Signatures

MetaProb v2

:: DESCRIPTION

MetaProb is a novel assembly-assisted tool for unsupervised metagenomic binning.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MetaProb 

:: MORE INFORMATION

Citation

Bioinformatics, 32 (17), i567-i575 2016 Sep 1
MetaProb: Accurate Metagenomic Reads Binning Based on Probabilistic Sequence Signatures
Samuele Girotto 1, Cinzia Pizzi 1, Matteo Comin 1

Arachne 4.6233 – Whole-genome Shotgun Assembler

Arachne 4.6233

:: DESCRIPTION

ARACHNE is a program for assembling data from whole genome shotgun sequencing experiments. It was designed for long reads from Sanger sequencing technology, and has been used extensively to assemble many genomes, including many that are large and highly repetitive.

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Arachne

:: MORE INFORMATION

Citation

Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. 2002.
ARACHNE: a whole-genome shotgun assembler.
Genome Research12: 177–189.

Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. 2003.
Whole-genome sequence assembly for mammalian genomes: Arachne 2.
Genome Research 13: 91–96.

Gnerre S, Lander ES, Lindblad-Toh K, Jaffe DB. 2009.
Assisted assembly: how to improve a de novo genome assembly by using related species.
Genome Biology10: R88.

MetaCompass v2.0-beta – Reference-guided Assembly of Metagenomes

MetaCompass v2.0-beta

:: DESCRIPTION

MetaCompass represents the first effective approach for reference-guided metagenomic assembly of low-abundance bacterial genomes that can complement and improve upon de novo metagenomic assembly methods.

::DEVELOPER

Treangen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

MetaCompass

:: MORE INFORMATION

MetAMOS 1.5rc3 – Metagenomic Assembly pipeline for AMOS

MetAMOS 1.5rc3

:: DESCRIPTION

MetAMOS is an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations.

::DEVELOPER

Treangen Lab

:: SCREENSHOTS

MetAMOS 

:: REQUIREMENTS

  • Linux
  • Java
  • Perl 

:: DOWNLOAD

 MetAMOS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 May 3;15:126. doi: 10.1186/1471-2105-15-126.
Automated ensemble assembly and validation of microbial genomes.
Koren S1, Treangen TJ, Hill CM, Pop M, Phillippy AM.

Genome Biol. 2013 Jan 15;14(1):R2.
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.
Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M.

A5-miseq 20160825 – de novo Assembly & Analysis of Illumina Sequence data

A5-miseq 20160825

:: DESCRIPTION

de novo assembly & analysis of Illumina sequence data, including the A5 pipeline, A5-miseq, tools to evaluate assembly quality, and scripts to facilitate data submission to NCBI and the RAST annotation system

::DEVELOPER

The Darling Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 A5-miseq

:: MORE INFORMATION

Citation

A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data.
Coil D, Jospin G, Darling AE.
Bioinformatics. 2014 Oct 22. pii: btu661.

PEAssember 1.2 – A de novo Genome Assembler

PEAssember 1.2

:: DESCRIPTION

PEAssember is a parallel de novo genome assembler for small – mid sized genomes.

::DEVELOPER

Pramila Nuwantha Ariyaratne, Sung Wing Kin, Ken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • C++ Compiler

:: DOWNLOAD

 PEAssember

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jan 15;27(2):167-74. doi: 10.1093/bioinformatics/btq626. Epub 2010 Dec 12.
PE-Assembler: de novo assembler using short paired-end reads.
Ariyaratne PN, Sung WK.

SSP – de novo Transcriptome Assembler

SSP

:: DESCRIPTION

SSP is a de novo transcriptome assembler that assembles RNA-seq reads into transcripts. SSP aims to reconstructs all the alternatively spliced isoforms and estimates the expression level of them.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/Linux

:: DOWNLOAD

 SSP

:: MORE INFORMATION

SAMMate 2.7.4 / assemblySAM 1.1 – Processing Short Read Alignments in SAM/BAM format / RNA-Seq Assembly and Analysis

SAMMate 2.7.4 / assemblySAM 1.1

:: DESCRIPTION

SAMMate is an open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.

assemblySAM employs a novel method to localize and assemble RNA-seq reads into RNA transcript sequences.

::DEVELOPER

Dongxiao Zhu, Ph.D

:: SCREENSHOTS

sammate

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java
  • R package

:: DOWNLOAD

 SAMMate / assemblySAM

:: MORE INFORMATION

Citation:

Source Code Biol Med. 2011 Jan 13;6(1):2. doi: 10.1186/1751-0473-6-2.
SAMMate: a GUI tool for processing short read alignments in SAM/BAM format.
Xu G1, Deng N, Zhao Z, Judeh T, Flemington E, Zhu D.

Nguyen, T, Zhao, Z, Zhu, D.
SPATA: A seeding and patching algorithm for hybrid transcriptome assembly.

Nguyen, T, Deng, N, Zhu, D.
SASeq: A selective and adaptive shrinkage approach to detect and quantify active transcripts using RNA-Seq.