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.

GMASS – Genome Assembly Structural Similarity

GMASS

:: DESCRIPTION

The GMASS score is a novel measure for representing structural similarity between two assemblies. It represents the structural similarity of a pair of assemblies based on the length and number of similar genomic regions defined as consensus segment blocks (CSBs) in the assemblies.

::DEVELOPER

Bioinformatics Laboratory, Konkuk University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

GMASS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2019 Mar 18;20(1):147. doi: 10.1186/s12859-019-2710-z.
GMASS: a novel measure for genome assembly structural similarity.
Kwon D, Lee J, Kim J.

IMAP – Chromosome-level Genome Assembler Combining multiple de novo Assemblies

IMAP

:: DESCRIPTION

IMAP (the integrative meta-assembly pipeline) is a new software pipeline to build chromosome-level genome sequence assemblies by generating and combining multiple initial assemblies using three de novo assemblers from short-read sequencing data.

::DEVELOPER

Bioinformatics Laboratory, Konkuk University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java
  • Python
  • Perl

:: DOWNLOAD

IMAP

:: MORE INFORMATION

Citation

PLoS One. 2019 Aug 27;14(8):e0221858. doi: 10.1371/journal.pone.0221858. eCollection 2019.
Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies.
Song G, Lee J, Kim J, Kang S, Lee H, Kwon D, Lee D, Lang GI, Cherry JM, Kim J.

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.

RACA – Reference-Assisted Chromosome Assembly

RACA

:: DESCRIPTION

RACA is an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RACA

:: MORE INFORMATION

Citation

Reference-assisted chromosome assembly.
Kim J, Larkin DM, Cai Q, Asan, Zhang Y, Ge RL, Auvil L, Capitanu B, Zhang G, Lewin HA, Ma J.
Proc Natl Acad Sci U S A. 2013 Jan 29;110(5):1785-90. doi: 10.1073/pnas.1220349110

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.

FASeg 2.0 – Forward Backward Fragment Assembling Segmentation

 

FASeg 2.0

:: DESCRIPTION

FASeg is an R package that performs forward-backward fragment assembling segmentation for array-CGH and SNP array data

::DEVELOPER

Tianwei Yu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

FASeg

:: MORE INFORMATION

Citation

A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array.
Yu T, Ye H, Sun W, Li KC, Chen Z, Jacobs S, Bailey DK, Wong DT, Zhou X.
BMC Bioinformatics. 2007 May 3;8:145.