PRICE 1.2 – de novo Genome Assembler

PRICE 1.2

:: DESCRIPTION

PRICE (Paired-Read Iterative Contig Extension) is a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the size of existing contigs. Initially, those contigs can be individual reads from a subset of the paired-read dataset, non-paired reads from sequencing technologies that provide non-paired data, or contigs that were output from a prior run of PRICE or any other assembler.

::DEVELOPER

DeRisi Lab, UCSF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

PRICE

:: MORE INFORMATION

Citation

PRICE: Software for the Targeted Assembly of Components of (Meta)Genomic Sequence Data
J. Graham Ruby, Priya Bellare and Joseph L. DeRisi
G3 March 23, 2013 g3.113.005967

YASRA 2.33 – Yet Another Short Read Assembler

YASRA 2.33

:: DESCRIPTION

YASRA performs comparative assembly of short reads using a reference genome, which can differ substantially from the genome being sequenced.

::DEVELOPER

Aakrosh Ratan (ratan@bx.psu.edu) at Miller Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
LASTZ

:: DOWNLOAD

YASRA

:: MORE INFORMATION

Citation

Ratan, Aakrosh
Assembly algorithms for next-generation sequencing data.

AutoAssemblyD 0.1 – Graphical User Interface system for several Genome Assembler

AutoAssemblyD 0.1

:: DESCRIPTION

The AssemblyD is a software which performed the local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers.

::DEVELOPER

AutoAssemblyD team

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux/MacOsX
Java

:: DOWNLOAD

AutoAssemblyD

:: MORE INFORMATION

Citation

Bioinformation. 2013 Sep 23;9(16):840-1. doi: 10.6026/97320630009840. eCollection 2013.
AutoAssemblyD: a graphical user interface system for several genome assemblers.
Veras AA1, de Sá PH, Azevedo V, Silva A, Ramos RT.

ASA3P v1.3.0 – Automatic Bacterial Isolate Assembly, Annotation and Analyses Pipeline

ASA3P v1.3.0

:: DESCRIPTION

ASA3P is an automatic and highly scalable assembly, annotation and higher-level analyses pipeline for closely related bacterial isolates.

::DEVELOPER

Bioinformatics and Systems Biology, Justus-Liebig-University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Docker / OpenStack

:: DOWNLOAD

ASA3P

:: MORE INFORMATION

Citation

Schwengers O, Hoek A, Fritzenwanker M, Falgenhauer L, Hain T, Chakraborty T, Goesmann A.
ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates.
PLoS Comput Biol. 2020 Mar 5;16(3):e1007134. doi: 10.1371/journal.pcbi.1007134. PMID: 32134915; PMCID: PMC7077848.

ARCS / ARKS v1.2.2 – Genome Assembly Scaffolder with linked and Long Reads

ARCS / ARKS v1.2.2

:: DESCRIPTION

ARCS is a genomics software for scaffolding genome assembly drafts using linked or long reads.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

ARCS

:: MORE INFORMATION

Citation

Coombe L, Zhang J, Vandervalk BP, Chu J, Jackman SD, Birol I, Warren RL.
ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.
BMC Bioinformatics. 2018 Jun 20;19(1):234. doi: 10.1186/s12859-018-2243-x. PMID: 29925315; PMCID: PMC6011487.

ABySS 2.3.2 – de novo, parallel, paired-end Sequence Assembler

ABySS 2.3.2

:: DESCRIPTION

ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/MacOsX

:: DOWNLOAD

ABySS

:: MORE INFORMATION

Citation

Paulino D, Warren RL, Vandervalk BP, Raymond A, Jackman SD, Birol I.
Sealer: a scalable gap-closing application for finishing draft genomes.
BMC Bioinformatics. 2015 Jul 25;16(1):230. doi: 10.1186/s12859-015-0663-4. PMID: 26209068; PMCID: PMC4515008.

Vandervalk BP, Yang C, Xue Z, Raghavan K, Chu J, Mohamadi H, Jackman SD, Chiu R, Warren RL, Birol I.
Konnector v2.0: pseudo-long reads from paired-end sequencing data.
BMC Med Genomics. 2015;8 Suppl 3(Suppl 3):S1. doi: 10.1186/1755-8794-8-S3-S1. Epub 2015 Sep 23. PMID: 26399504; PMCID: PMC4582294.

Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.
ABySS: A parallel assembler for short read sequence data.
Genome Res. 2009. 19: 1117-1123

KLEAT 2.0 – Identifies 3′ UTR Ends of Transcripts in de novo RNA-Seq Assemblies

KLEAT 2.0

:: DESCRIPTION

KLEAT is a post-processing tool for CLEavage site Analysis of Transcriptomes. KLEAT is designed to work on trans-ABySS output.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/MacOsX
Python

:: DOWNLOAD

KLEAT

:: MORE INFORMATION

Citation

Birol I, Raymond A, Chiu R, Nip KM, Jackman SD, Kreitzman M, Docking TR, Ennis CA, Robertson AG, Karsan A.
Kleat: cleavage site analysis of transcriptomes.
Pac Symp Biocomput. 2015:347-58. PMID: 25592595; PMCID: PMC4350765.

CSAR / Multi-CSAR – Contig Scaffolding tool using Algebraic Rearrangements

CSAR / Multi-CSAR

:: DESCRIPTION

CSAR is a contig scaffolding tool that can efficiently and accurately scaffold the contigs of a draft genome (i.e., target genome) based on an incomplete reference genome of a related organism.

Multi-CSAR is a multiple reference-based contig scaffolder using algebraic rearrangements

::DEVELOPER

Chin Lung Lu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
PHP

:: DOWNLOAD

CSAR / Multi-CSAR

:: MORE INFORMATION

Citation

Chen KT, Shen HT, Lu CL.
Multi-CSAR: a multiple reference-based contig scaffolder using algebraic rearrangements.
BMC Syst Biol. 2018 Dec 31;12(Suppl 9):139. doi: 10.1186/s12918-018-0654-y. PMID: 30598087; PMCID: PMC6311912.

Chen KT, Lu CL.
CSAR-web: a web server of contig scaffolding using algebraic rearrangements.
Nucleic Acids Res. 2018 Jul 2;46(W1):W55-W59. doi: 10.1093/nar/gky337. PMID: 29733393; PMCID: PMC6030906.

Chen KT, Liu CL, Huang SH, Shen HT, Shieh YK, Chiu HT, Lu CL.
CSAR: a contig scaffolding tool using algebraic rearrangements.
Bioinformatics. 2018 Jan 1;34(1):109-111. doi: 10.1093/bioinformatics/btx543. PMID: 28968788.

CAR – Contig Assembly of Prokaryotic Draft Genomes Using Rearrangements

CAR

:: DESCRIPTION

CAR is an efficient and more accurate tool for assembling contigs of a prokaryotic draft genome based on a reference genome.

::DEVELOPER

Chin Lung Lu,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Nov 28;15(1):381.
CAR: contig assembly of prokaryotic draft genomes using rearrangements.
Lu C, Chen KT, Huang SY, Chiu HT.

Tigmint v1.2.4 – Correct Misassemblies using linked AND long reads

Tigmint v1.2.4

:: DESCRIPTION

Tigmint identifies and corrects misassemblies in genomes using linked (e.g. MGI’s stLFR, 10x Genomics Chromium) or long (e.g. Oxford Nanopore Technologies long reads) DNA sequencing reads.

::DEVELOPER

BC Cancer Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Tigmint

:: MORE INFORMATION

Citation

Jackman SD, Coombe L, Chu J, Warren RL, Vandervalk BP, Yeo S, Xue Z, Mohamadi H, Bohlmann J, Jones SJM, Birol I.
Tigmint: correcting assembly errors using linked reads from large molecules.
BMC Bioinformatics. 2018 Oct 26;19(1):393. doi: 10.1186/s12859-018-2425-6. PMID: 30367597; PMCID: PMC6204047.