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.

HapTree 1.0 – Polyploid Haplotype Assembly tool

HapTree 1.0

:: DESCRIPTION

HapTree is a polyploid haplotype assembly tool based on a statistical framework.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

  HapTree

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2014 Mar 27;10(3):e1003502. doi: 10.1371/journal.pcbi.1003502. eCollection 2014.
HapTree: a novel Bayesian framework for single individual polyplotyping using NGS data.
Berger E, Yorukoglu D, Peng J, Berger B

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

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.

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.

TIGER – DNA Sequence Assembly

TIGER

:: DESCRIPTION

Tiger is a novel de novo assembly framework  which adapts to available computing resources by iteratively decomposing the assembly problem into sub-problems.

::DEVELOPER

IMPACT Reach Group (Illinois Microarchitecture Project using Algorithms and Compiler Technology)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 TIGER

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012;13 Suppl 19:S18. doi: 10.1186/1471-2105-13-S19-S18. Epub 2012 Dec 19.
TIGER: tiled iterative genome assembler.
Wu XL1, Heo Y, El Hajj I, Hwu WM, Chen D, Ma J.

ALE 20180904 – Assembly Likelihood Estimator

ALE 20180904

:: DESCRIPTION

ALE is a probabalistic framework for determining the likelihood of an assembly given the data (raw reads) used to assemble it. It allows for the rapid discovery of errors and comparisons between similar assemblies.

::DEVELOPER

Scott Clark@Cornell University Center for Applied Mathematics, Rob Egan@Department of Energy Joint Genome Institute

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX
  • C Compiler
  • Python

:: DOWNLOAD

 ALE

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 15;29(4):435-43. doi: 10.1093/bioinformatics/bts723. Epub 2013 Jan 9.
ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies.
Clark SC, Egan R, Frazier PI, Wang Z.

Rnnotator 3.5.0 – de novo Transcriptome Assembly pipeline from stranded RNA-Seq reads

Rnnotator 3.5.0

:: DESCRIPTION

Rnnotator is an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome.

::DEVELOPER

Zhong Wang at U.S. Department of Energy Joint Genome Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • BioPerl
  • Blat

:: DOWNLOAD

  Rnnotator

:: MORE INFORMATION

Citation

BMC Genomics. 2010 Nov 24;11:663. doi: 10.1186/1471-2164-11-663.
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads.
Martin J, Bruno VM, Fang Z, Meng X, Blow M, Zhang T, Sherlock G, Snyder M, Wang Z.

TRUST4 v0.1.1 – TCR and BCR Assembly from RNA-seq data

TRUST4 v0.1.1

:: DESCRIPTION

TRUST (T cell receptor Repertoire Utilities for Solid Tissue/Tumor) is a toolbox for analyzing T cell receptors in solid tumors using unselected RNA-seq data based on de novo assembly.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

TRUST

:: MORE INFORMATION