Tag: assembler

SRAssembler v1.0.0 – Selective and Recursive local Assembler

SRAssembler v1.0.0

:: DESCRIPTION

SRAssembler is a modular pipeline program that can assemble genomic DNA reads into contigs that are homologous to a query DNA or protein sequence.

::DEVELOPER

The Brendel Group @ Indiana University

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SRAssembler

:: MORE INFORMATION

Citation

McCarthy TW, Chou HC, Brendel VP.
SRAssembler: Selective Recursive local Assembly of homologous genomic regions.
BMC Bioinformatics. 2019 Jul 2;20(1):371. doi: 10.1186/s12859-019-2949-4. PMID: 31266441; PMCID: PMC6604332.

PaKman – Parallel Genome Assembler for Scalable Generation of Genomic Contigs

PaKman

:: DESCRIPTION

PaKman is a scalable algorithm for generating genomic contigs on distributed memory machines.

::DEVELOPER

Ananth Kalyanaraman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

PaKman

:: MORE INFORMATION

Citation

Ghosh, Priyanka, Sriram Krishnamoorthy, and Ananth Kalyanaraman.
“PaKman: A Scalable Algorithm for Generating Genomic Contigs on Distributed Memory Machines.”
IEEE Transactions on Parallel and Distributed Systems (TPDS) vol. 32, no. 5, pp. 1191-1209, 2021. DOI: 10.1109/TPDS.2020.3043241.

CStone – de novo Transcriptome Assembler

CStone

:: DESCRIPTION

CStone is a de novo assembler for RNA-Seq data that uses de Bruijn like graphs and annotates each contig produced with one of three graph classification levels indicating whether or not it can be guaranteed to be non chimeric.

::DEVELOPER

John Archer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

CStone

:: MORE INFORMATION

Citation

Linheiro R, Archer J.
CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure.
PLoS Comput Biol. 2021 Nov 23;17(11):e1009631. doi: 10.1371/journal.pcbi.1009631. Epub ahead of print. PMID: 34813594.

Edena v3.131028 – De Novo Short Reads Assembler

Edena v3.131028

:: DESCRIPTION

Edena is an assembler dedicated to process the millions of very short reads produced by the Illumina Genome Analyzer

::DEVELOPER

D. Hernandez @ The Genomic Research Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Edena

:: MORE INFORMATION

Citation:

Hernandez D, François P, Farinelli L, Osterås, Schrenzel J.
De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.
Genome Research. 18:802-809, 2008.

HyAsP – Hybrid Assembler for Plasmids

HyAsP

:: DESCRIPTION

HyAsP is a tool for the extracting plasmids from WGS assemblies in an automatic way. It combines ideas from both reference-based and depth-based methods to identify plasmids in a greedy algorithm, using information on the occurrences of known plasmid genes and considering characteristics of the contigs such as read depth and GC content.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • conda

:: DOWNLOAD

HyAsP

:: MORE INFORMATION

Citation

Müller R, Chauve C.
HyAsP, a greedy tool for plasmids identification.
Bioinformatics. 2019 Nov 1;35(21):4436-4439. doi: 10.1093/bioinformatics/btz413. PMID: 31116364.

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

:: DOWNLOAD

 YASRA

:: MORE INFORMATION

Citation

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

HipMer 1.2.2 / MetaHipMer 2.0.1 – Extreme Scale De Novo Genome and MetaGenome Assembler

HipMer 1.2.2 / MetaHipMer 2.0.1

:: DESCRIPTION

HipMer is a high-performance application that produces high-quality de novo assemblies for very large-scale genomes.

The MetaHipMer extension is a recent addition to HipMer that is geared to large metagenomes and leverages iterative kmer sizes and a specialized scaffolding algorithm to produce increased contiguity and accuracy in metagenomic assemblies. It is able to reconstruct rRNA elements via a separate algorithm which relies on reference SSU and LSU Hidden Markov Models to help traverse the contig graph around ribosomal RNA regions.

::DEVELOPER

Berkeley Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

HipMer / MetaHipMer

:: MORE INFORMATION

Citation

E. Georganas et al.,
“HipMer: an extreme-scale de novo genome assembler,”
SC ’15: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, 2015, pp. 1-11, doi: 10.1145/2807591.2807664.

Hofmeyr S, Egan R, Georganas E, Copeland AC, Riley R, Clum A, Eloe-Fadrosh E, Roux S, Goltsman E, Buluç A, Rokhsar D, Oliker L, Yelick K.
Terabase-scale metagenome coassembly with MetaHipMer.
Sci Rep. 2020 Jul 1;10(1):10689. doi: 10.1038/s41598-020-67416-5. PMID: 32612216; PMCID: PMC7329831.

VAGUE 1.0.5 – Velvet Assembler Graphical User Environment

VAGUE 1.0.5

:: DESCRIPTION

VAGUE (Velvet Assembler Graphical Front End) is a GUI for the Velvet de novo assembler.

::DEVELOPER

Victorian Bioinformatics Consortium

:: SCREENSHOTS

VAGUE

:: REQUIREMENTS

:: DOWNLOAD

 VAGUE 

:: MORE INFORMATION

Citation

Powell DR, Seemann T.
VAGUE: a graphical user interface for the Velvet assembler.
Bioinformatics. 2013 Jan 15;29(2):264-5. doi: 10.1093/bioinformatics/bts664. Epub 2012 Nov 17. PMID: 23162059.

Celera Assembler 8.3 / Canu v2.2 – Whole Genome Shotgun Assembler

Celera Assembler 8.3 / Canu v2.2

:: DESCRIPTION

Celera Assembler (wgs-assembler) is scientific software for DNA research. It can reconstruct long sequences of genomic DNA given the fragmentary data produced by whole-genome shotgun sequencing. The Celera Assembler has enabled discovery in microbial genomes, large eukaryotic genomes, diploid genomes, and genomes from environmental samples. Celera Assembler contributed the first diploid sequence of an individual human, and metagenomics assemblies of the Global Ocean Sampling

Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION).

::DEVELOPER

Celera Assembler team / Maryland Bioinformatics Labs (MarBL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Celera Assembler / Canu

:: MORE INFORMATION

Citation

Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM.
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
Genome Res. 2017 May;27(5):722-736. doi: 10.1101/gr.215087.116. Epub 2017 Mar 15. PMID: 28298431; PMCID: PMC5411767.

Denisov et al. (2008)
Consensus Generation and Variant Detection by Celera Assembler.
Bioinformatics 24(8):1035-40

AMOS 3.1.0 – Whole Genome Shotgun Assembler

AMOS 3.1.0

:: DESCRIPTION

AMOS (A Modular, Open-Source) consortium is committed to the development of open-source whole genome assembly software. The project acronym (AMOS) represents our primary goal — to produce A Modular, Open-Source whole genome assembler.Open-source so that everyone is welcome to contribute and help build outstanding assembly tools, and modular in nature so that new contributions can be easily inserted into an existing assembly pipeline. This modular design will foster the development of new assembly algorithms and allow the AMOS project to continually grow and improve in hopes of eventually becoming a widely accepted and deployed assembly infrastructure. In this sense, AMOS is both a design philosophy and a software system.

::DEVELOPER

AMOS Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

AMOS

:: MORE INFORMATION

Citation

Next generation sequence assembly with AMOS.
Treangen TJ, Sommer DD, Angly FE, Koren S, Pop M.
Curr Protoc Bioinformatics. 2011 Mar;Chapter 11:Unit 11.8. doi: 10.1002/0471250953.bi1108s33.