SuRankCo R5 – Supervised Ranking of Contigs in de novo Assemblies

SuRankCo R5

:: DESCRIPTION

SuRankCo is a machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet.

::DEVELOPER

SuRankCo team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
Java
R

:: DOWNLOAD

SuRankCo

:: MORE INFORMATION

Citation

Kuhring M, Dabrowski PW, Piro VC, Nitsche A, Renard BY.
SuRankCo: supervised ranking of contigs in de novo assemblies.
BMC Bioinformatics. 2015 Jul 30;16:240. doi: 10.1186/s12859-015-0644-7. PMID: 26224355; PMCID: PMC4520199.

CCBuilder 2.0.4 – Coiled-coil Protein Assemblies

CCBuilder 2.0.4

:: DESCRIPTION

CCBuilder is a web-based application that tackles the problem for a defined but large class of protein structure, the α-helical coiled coils.

::DEVELOPER

Woolfson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

CCBuilder

:: MORE INFORMATION

Citation

Wood CW, Woolfson DN.
CCBuilder 2.0: Powerful and accessible coiled-coil modeling.
Protein Sci. 2018 Jan;27(1):103-111. doi: 10.1002/pro.3279. Epub 2017 Sep 15. PMID: 28836317; PMCID: PMC5734305.

CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies.
Wood CW, Bruning M, Ibarra AA, Bartlett GJ, Thomson AR, Sessions RB, Brady RL, Woolfson DN.
Bioinformatics. 2014 Jul 26. pii: btu502.

PACVr 0.9.4 – Plastome Assembly Coverage Visualization in R

PACVr 0.9.4

:: DESCRIPTION

PACVr visualizes the coverage depth of a complete plastid genome as well as the equality of its inverted repeat regions in relation to the circular, quadripartite genome structure and the location of individual genes.

::DEVELOPER

Michael Gruenstaeudl

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux / MacOs
R

:: DOWNLOAD

PACVr

:: MORE INFORMATION

Citation

Gruenstaeudl M, Jenke N.
PACVr: plastome assembly coverage visualization in R.
BMC Bioinformatics. 2020 May 24;21(1):207. doi: 10.1186/s12859-020-3475-0. PMID: 32448146; PMCID: PMC7245912.

HomeoSplitter 1.01 – Disentangling Homeologous Contigs in Allo-tetraploid Assembly

HomeoSplitter 1.01

:: DESCRIPTION

HomeoSplitter is a fast and effective solution to disentangle homeologous sequences based on a maximum likelihood optimization.

::DEVELOPER

HomeoSplitter team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
Java

:: DOWNLOAD

HomeoSplitter

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 15:S15. doi: 10.1186/1471-2105-14-S15-S15. Epub 2013 Oct 15.
Disentangling homeologous contigs in allo-tetraploid assembly: application to durum wheat.
Ranwez V, Holtz Y, Sarah G, Ardisson M, Santoni S, Glémin S, Tavaud-Pirra M, David J.

AceParser 1.33 – Parse an Ace file (Phred/Phrap output) into a tab-delimited Assembly Alignment file

AceParser 1.33

:: DESCRIPTION

AceParser: Parse an Ace file (Phred/Phrap output) into a tab-delimited assembly alignment file. Options to include embedded annotation from multiple sources.

::DEVELOPER

J. Cris Vera

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

AceParser

:: MORE INFORMATION

SimAssemblyStage1/2 0.2 – Assembly Alignment of Contigs

SimAssemblyStage1/2 0.2

:: DESCRIPTION

SimAssemblyStage1: Perfectly aligns TranscriptSimulator reads to their nucleotide templates using read title inforamation, creating ideal simulated assembly of super contigs.

SimAssemblyStage2: Creates an optimal simulated assembly alignment of contigs using the output of SimAssemblyStage1.

::DEVELOPER

J. Cris Vera

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

SimAssemblyStage1/2

:: MORE INFORMATION

GRASP 0.0.4 – Guided Reference-based Assembly of Short Peptides

GRASP 0.0.4

:: DESCRIPTION

GRASP is a gene annotation tool for metagenomic studies. GRASP assembles the fragmented short-peptides, which are called from the NGS reads, and aligns the assembled contigs to the query reference protein. GRASP achieves much higher sensitivity than BLASTP for gene annotation purpose.

::DEVELOPER

GRASP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

GRASP

:: MORE INFORMATION

Citation

GRASP: Guided Reference-based Assembly of Short Peptides.
Zhong C, Yang Y, Yooseph S.
Nucleic Acids Res. 2014 Nov 20. pii: gku1210

Bridger 20141201 – RNA-Seq Assembly

Bridger 20141201

:: DESCRIPTION

Bridger is a new de novo transcriptome assembler which takes advantage of techniques employed in Cufflinks to overcome limitations of the existing de novo assemblers.

::DEVELOPER

Bridger team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Bridger

:: MORE INFORMATION

Citation:

Genome Biol. 2015 Feb 11;16:30. doi: 10.1186/s13059-015-0596-2.
Bridger: a new framework for de novo transcriptome assembly using RNA-seq data.
Chang Z, Li G, Liu J, Zhang Y, Ashby C, Liu D, Cramer CL, Huang X.

VTBuilder – Assembly of Multi Isoform Transcriptomes

VTBuilder

:: DESCRIPTION

VTBuilder is a tool for the inference of non-chimeric contigs from read data that has been sequenced from complex multi-isoformic transcriptomes, such as snake venom glands, or rapidly evolving viral populations, such as HIV-1.

::DEVELOPER

VTBuilder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
JRE

:: DOWNLOAD

VTBuilder

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Dec 3;15(1):389.
VTBuilder: a tool for the assembly of multi isoform transcriptomes.
Archer JP, Whiteley G, Casewell NR, Harrison RA, Wagstaff SC.

aTRAM 2.4.3 – automated Target Restricted Assembly Method

aTRAM 2.4.3

:: DESCRIPTION

aTRAM performs targeted de novo assembly of loci from paired-end Illumina runs.

::DEVELOPER

aTRAM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
Perl

aTRAM

:: MORE INFORMATION

Citation

aTRAM – automated target restricted assembly method: a fast method for assembling loci across divergent taxa from next-generation sequencing data.
Allen JM, Huang DI, Cronk QC, Johnson KP.
BMC Bioinformatics. 2015 Mar 25;16(1):98.