LASER – Large genome ASsembly EvaluatoR

LASER

:: DESCRIPTION

LASER is based on QUAST genome assembly program and provides huge performance improvements for large genomes.

::DEVELOPER

LUCIAN ILIE

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

LASER

:: MORE INFORMATION

Citation

LASER: Large genome ASsembly EvaluatoR.
Khiste N, Ilie L.
BMC Res Notes. 2015 Nov 24;8:709. doi: 10.1186/s13104-015-1682-y.

SAGE 2 – String Graph Assembly of GEnomes

SAGE 2

:: DESCRIPTION

SAGE is a new string-overlap graph-based de novo genome assembler.

::DEVELOPER

LUCIAN ILIE

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SAGE

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Sep 15;15:302. doi: 10.1186/1471-2105-15-302.
SAGE: String-overlap Assembly of GEnomes.
Ilie L1, Haider B, Molnar M, Solis-Oba R.

SAVAGE 0.4.0 – Strain Aware VirAl GEnome assembly

SAVAGE 0.4.0

:: DESCRIPTION

SAVAGE is a computational tool for reconstructing individual haplotypes of intra-host virus strains (a viral quasispecies) without the need for a high quality reference genome.

::DEVELOPER

SAVAGE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  SAVAGE

:: MORE INFORMATION

Citation:

Genome Res. 2017 May;27(5):835-848. doi: 10.1101/gr.215038.116. Epub 2017 Apr 10.
De novo assembly of viral quasispecies using overlap graphs.
Baaijens JA, Aabidine AZE, Rivals E, Schönhuth A.

RaGOO v1.11 – Fast Reference-Guided Scaffolding of Genome Assembly Contigs

RaGOO v1.11

:: DESCRIPTION

RaGOO is a tool to order and orient genome assembly contigs via Minimap2 alignments to a reference genome.

::DEVELOPER

RaGOO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / OSX
  • Python

:: DOWNLOAD

RaGOO

:: MORE INFORMATION

Citation

RaGOO: fast and accurate reference-guided scaffolding of draft genomes.
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC.
Genome Biol. 2019 Oct 28;20(1):224. doi: 10.1186/s13059-019-1829-6.

ARIBA 2.14.4 – Antimicrobial Resistance Identification By Assembly

ARIBA 2.14.4

:: DESCRIPTION

ARIBA is a tool that identifies antibiotic resistance genes by running local assemblies.

::DEVELOPER

Pathogen Informatics, Wellcome Trust Sanger Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

ARIBA

:: MORE INFORMATION

Citation

J Glob Antimicrob Resist. 2019 Sep 7;19:129-131. doi: 10.1016/j.jgar.2019.09.001. [Epub ahead of print]
Draft genome of a macrolide resistant XDR Salmonella enterica serovar Paratyphi A strain using a shotgun sequencing approach.
Khatoon A, Malik HMT, Aurongzeb M, Raza SA, Karim A.

TAG 0.91 – Transcript Assembly by Mapping Reads to Graphs

TAG 0.91

:: DESCRIPTION

TAG is a tool for metatranscriptome assembly using de Bruijn graph of matched metagenome as the reference

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TAG

:: MORE INFORMATION

Citation:

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis.
Ye Y, Tang H.
Bioinformatics. 2015 Aug 29. pii: btv510.

AIDA – Ab Initio Domain Assembly Server

AIDA

:: DESCRIPTION

AIDA is a tool that can identify domains in multi-domain proteins and then predict their 3D structures and relative spatial arrangements.

::DEVELOPER

Godzik Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 AIDA

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W308-13. doi: 10.1093/nar/gku369. Epub 2014 May 15.
AIDA: ab initio domain assembly server.
Xu D, Jaroszewski L, Li Z, Godzik A

DETONATE 1.11 – DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation

DETONATE 1.11

:: DESCRIPTION

DETONATE consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences.

::DEVELOPER

Colin Dewey

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DETONATE

:: MORE INFORMATION

Citation

Genome Biol. 2014 Dec 21;15(12):553. doi: 10.1186/s13059-014-0553-5.
Evaluation of de novo transcriptome assemblies from RNA-Seq data.
Li B, Fillmore N, Bai Y, Collins M, Thomson JA, Stewart R, Dewey CN.

Trinity 2.8.6 – RNA-Seq De novo Assembly

Trinity 2.8.6

:: DESCRIPTION

Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • Java

:: DOWNLOAD

Trinity

:: MORE INFORMATION

Citation

Manfred G. Grabherr, Brian J. Haas, […], and Aviv Regev
Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data
Nat Biotechnol. 2011 May 15; 29(7): 644–652. doi: 10.1038/nbt.1883

BinPacker 1.1 – Packing-Based De Novo Transcriptome Assembly from RNA-seq Data

BinPacker 1.1

:: DESCRIPTION

BinPacker is a novel de novo assembler by modeling the transcriptome assembly problem as tracking a set of trajectories of items with their sizes representing coverage of their corresponding isoforms by solving a series of bin-packing problems.

::DEVELOPER

BinPacker team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BinPacker

:: MORE INFORMATION

Citation

BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data.
Liu J, Li G, Chang Z, Yu T, Liu B, McMullen R, Chen P, Huang X.
PLoS Comput Biol. 2016 Feb 19;12(2):e1004772. doi: 10.1371/journal.pcbi.1004772.