Category: Assembly Tools

BEAP 0.6 beta – Blast Extension and Assembly Program

BEAP 0.6 beta

:: DESCRIPTION

The BEAP is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as “primer”, to recursively blast nucleotide databases in an attempt to obtain all sequences that overlaps, directly or indirectly, with the “primer” therefore help to “extend” the length of the original sequence for constructing a “full length” sequence for functional analysis, or at least to obtain neighboring regions of the segment for SNP discovery and linkage disequilibrium analysis.

::DEVELOPER

NAGRP Bioinformatics Team

:: SCREENSHOTS

BEAP

:: REQUIREMENTS

  • Linux / Mac OsX/ WIndows
  • Perl
  • Java
  • NCBI Blast
  • CAP3

:: DOWNLOAD

 BEAP

:: MORE INFORMATION

Citation

James E. Koltes, Zhi-Liang Hu, Eric Fritz and James M. Reecy (2009).
BEAP: The BLAST Extension and Alignment Program — a tool for contig construction and analysis of preliminary genome sequence.
BMC Research Notes 2009, 2:11

BRANCH 1.8.1 – boosting RNA-Seq Assemblies with Partial or related Genomic Sequences

BRANCH 1.8.1

:: DESCRIPTION

BRANCH is a software that extends de novo transfrags and identifies novel transfrags with DNA contigs or genes of close related species. BRANCH discovers novel exons first and then extends/joins fragmented de novo transfrags, so that the resulted transfrags are more complete.

::DEVELOPER

Girke Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

:: DOWNLOAD

  BRANCH

:: MORE INFORMATION

Citation

BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences
Ergude Bao, Tao Jiang and Thomas Girke (2013)
Bioinformatics (2013) 29 (10): 1250-1259.doi: 10.1093/bioinformatics/btt127

Quake 0.3.5 – Detect & Correct Substitution Sequencing Errors in WGS Data Sets

Quake 0.3.5

:: DESCRIPTION

Quake is a package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads. Quake adopts the k-mer error correction framework, first introduced by the EULER genome assembly package. Unlike EULER and similar progams, Quake utilizes a robust mixture model of erroneous and genuine k-mer distributions to determine where errors are located. Then Quake uses read quality values and learns the nucleotide to nucleotide error rates to determine what types of errors are most likely. This leads to more corrections and greater accuracy, especially with respect to avoiding mis-corrections,  which create false sequence unsimilar to anything in the original genome sequence from which the read was taken.

::DEVELOPER

Center for Computational Biology , Johns Hopkins University School of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Quake

:: MORE INFORMATION

Citation

Genome Biology 2010, 11:R116
Quake: quality-aware detection and correction of sequencing errors
David R Kelley, Michael C Schatz and Steven L Salzberg

Lucy 2.20 – DNA Sequence Quality & Vector Trimming

Lucy 2.20

:: DESCRIPTION

Lucy has been used for several years to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses.  The quality trimming portion of lucy makes use of phred quality scores, such as those produced by many automated sequencers based on the Sanger sequencing method.  As such, lucy’s quality trimming may not be appropriate for sequence data produced by some of the new “next-generation” sequencers.

lucy1 Website

::DEVELOPER

the J. Craig Venter Institute/ Complex Computation Laboratory ,Iowa State University

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /Mac OsX

:: DOWNLOAD

Registration First, Lucy

:: MORE INFORMATION

Citation

1. LUCY2: an interactive DNA sequence quality trimming and vector removal tool

Bioinformatics Advance Access published on May 6, 2004
Song Li and Hui-Hsien Chou Bioinformatics, Nov 2004; 20: 2865-2866.

 

2. DNA sequence quality trimming and vector removal
Hui-Hsien Chou and Michael H. Holmes.Bioinformatics. 2001. 17(12):1093-1104.

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

GAEMR 1.0.1 – Assembly Analysis Framework

GAEMR 1.0.1

:: DESCRIPTION

GAEMR (Genome Assembly Evaluation Metrics and Reportin) is a complete genome analysis package that helps you evaluate and report on a genome assembly’s completeness, correctness, and contiguity.

::DEVELOPER

Broad Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GAEMR

:: MORE INFORMATION

PyroCleaner 1.3 – Clean 454 Pyrosequencing Reads in order to ease the Assembly Process

PyroCleaner 1.3

:: DESCRIPTION

The pyrocleaner is intended to clean the reads included in the sff file in order to ease the assembly process. It enables filtering sequences on different criteria such as length, complexity, number of undetermined bases which has been proven to correlate with poor quality and multiple copy reads. It also enables to clean paired-ends sff files and generates on one side a sff with the validated paired-ends and on the other the sequences which can be used as shotgun reads.

::DEVELOPER

the bioinformatic plateforms of Genotoul.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  PyroCleaner

:: MORE INFORMATION

Citation

Mariette J, Noirot C, Klopp C.
Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool.
BMC Research Notes 2011, 4:149

Reconciliator 2.0 – The tool for Merging Assemblies

Reconciliator 2.0

:: DESCRIPTION

Reconciliator is the tool for merging assemblies.

::DEVELOPER

IPST GENOME ASSEMBLY GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Reconciliator

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Jan 1;24(1):42-5. Epub 2007 Dec 5.
Assembly reconciliation.
Zimin AV, Smith DR, Sutton G, Yorke JA.

PhrapUMD 2 – Modified version of Phrap

PhrapUMD 2

:: DESCRIPTION

Phrap UMD consists of the UMD Trimmer, UMD Overlapper and a modified version of Phrap.It is capable of assembling data downloaded directly from the NCBI Trace Archive. The pipeline runs in 3 stages:  first the vector ends of the reads are examined and the vector is found.  Then the reads are trimmed for vector and quality.  After that the trimmed reads afe fed into the 5-pass UMD Overlapper that finds the overlaps, corrects the base caller errors and performs additional trimming if necessary.  After the overlaps are produced, the trimmed and error-corrected reads and overlaps are input into the modified version of Phrap, whichonly puts the reads together if they overlap according to the list of overlaps produced by the UMD Overlapper.

::DEVELOPER

IPST GENOME ASSEMBLY GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PhrapUMD

:: MORE INFORMATION

Citation:

PLoS One. 2008 Mar 19;3(3):e1836.
Improving Phrap-based assembly of the rat using “reliable” overlaps.
Roberts M, Zimin AV, Hayes W, Hunt BR, Ustun C, White JR, Havlak P, Yorke J.

DNA Dragon 1.5.6 build1 – DNA Sequence Contig Assembler Software

DNA Dragon 1.5.6 build1

:: DESCRIPTION

DNA Dragon Contig Assembler assembles sequences, trace data (ABI, SCF, AB1), Illumina and Roche 454 flowgrams into contigs. It is a very fast and accurate DNA sequence assembly software. The DNA sequences are assembled into contigs and a direct comparision of trace date with nucleotide data is possible. It also allows for proofreading and base editing.

::DEVELOPER

SequentiX

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

DNA Dragon

:: MORE INFORMATION