Tag: de novo Assembly

Bandage v0.8.1 – Navigating De novo Assembly Graphs Easily

Bandage v0.8.1

:: DESCRIPTION

Bandage (a B: ioinformatics A: pplication for N: avigating De novo A: ssembly G: raphs E: asily)  is a GUI program that allows users to interact with the assembly graphs made by de novo assemblers Velvet and SPAdes.

::DEVELOPER

Ryan Wick rrwick@gmail.com

:: SCREENSHOTS

Bandage

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX

:: DOWNLOAD

 Bandage

:: MORE INFORMATION

Citation:

Bandage: interactive visualisation of de novo genome assemblies.
Wick RR, Schultz MB, Zobel J, Holt KE.
Bioinformatics. 2015 Jun 22. pii: btv383

FermiKit 0.13 / fermi-lite 0.1- De novo Assembly based Variant Calling pipeline for Illumina Short Reads

FermiKit 0.13 / fermi-lite 0.1

:: DESCRIPTION

FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.

fermi-lite is a standalone C library as well as a command-line tool for assembling Illumina short reads in regions from 100bp to 10 million bp in size. Fermi-lite is largely a miniature of FermiKit.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FermiKit , fermi-lite

:: MORE INFORMATION

Citation

FermiKit: assembly-based variant calling for Illumina resequencing data.
Li H.
Bioinformatics. 2015 Nov 15;31(22):3694-6. doi: 10.1093/bioinformatics/btv440.

ELOPER 1.2 – Elongation of Paired-end Reads for de novo Assembly

ELOPER 1.2

:: DESCRIPTION

ELOPER is a pre-processing tool for pair-end sequences that produces a better read library for assembly programs.

::DEVELOPER

YanaiLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Perl / C++ Compiler

:: DOWNLOAD

 ELOPER

:: MORE INFORMATION

Citation:

ELOPER: elongation of paired-end reads as a pre-processing tool for improved de novo genome assembly.
Silver DH, Ben-Elazar S, Bogoslavsky A, Yanai I.
Bioinformatics. 2013 Jun 1;29(11):1455-7. doi: 10.1093/bioinformatics/btt169.

FinisherSC 2.1 – A Repeat-aware tool for upgrading de-novo Assembly using Long Reads

FinisherSC 2.1

:: DESCRIPTION

FinisherSC is a repeat-aware and scalable tool for upgrading de-novo assembly using long reads.

::DEVELOPER

Ka-Kit Lam

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 FinisherSC 

:: MORE INFORMATION

Citation

FinisherSC : A repeat-aware tool for upgrading de-novo assembly using long reads.
Lam KK, LaButti K, Khalak A, Tse D.
Bioinformatics. 2015 Jun 3. pii: btv280.

Recycler v0.7 – Detecting Plasmids from de novo Assembly Graphs

Recycler v0.7

:: DESCRIPTION

Recycler is a tool for extracting cyclical sequences from assembly graphs that are likely to be plasmids, phages, or other mobile elements that are physically separate from their host genomes. It can be applied on isolate, metagenome, and plasmidome graphs.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Recycler

:: MORE INFORMATION

Citation

Bioinformatics. 2017 Feb 15;33(4):475-482. doi: 10.1093/bioinformatics/btw651.
Recycler: an algorithm for detecting plasmids from de novo assembly graphs.
Rozov R, Brown Kav A, Bogumil D, Shterzer N, Halperin E, Mizrahi I, Shamir R.

Faucet v0.5 – Streaming de novo Assembly Graph Construction

Faucet v0.5

:: DESCRIPTION

Faucet is an streaming metagenome assembler. It uses low memory and disk space and achieves highly contiguous assemblies.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Faucet

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Jan 1;34(1):147-154. doi: 10.1093/bioinformatics/btx471.
Faucet: streaming de novo assembly graph construction.
Rozov R, Goldshlager G, Halperin E, Shamir R.

iAssembler 1.3.2 – de novo Assembly of Roche-454/Sanger Transcriptome Sequences

iAssembler 1.3.2

:: DESCRIPTION

iAssembler is a standalone package to assemble ESTs generated using Sanger and/or Roche-454 pyrosequencing technologies into contigs.

::DEVELOPER

Fei Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux
  • Perl
  • Bioperl

:: DOWNLOAD

 iAssembler

:: MORE INFORMATION

Citation

Zheng Y, Zhao L, Gao J, Fei Z. (2011)
iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences.
BMC Bioinformatics 12:453