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.

Tracembler – Contig Assembly Tool

Tracembler

:: DESCRIPTION

Tracembler takes one or multiple DNA or protein sequence(s) as input to the NCBI Trace Archive BLAST engine to identify matching sequence reads from a species of interest. The BLAST searches are carried out recursively such that BLAST matching sequences identified in previous rounds of searches are used as new queries in subsequent rounds of BLAST searches. Tracembler streamlines the process of recursive database searches, sequence assembly, and gene identification in resulting contigs in attempts to identify homologous loci of genes of interest in species with emerging whole genome shotgun reads.

::DEVELOPER

The Brendel Group @ Indiana University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Tracembler

:: MORE INFORMATION

Citation

Dong, Q., Wilkerson, M.D. & Brendel, V. (2007)
Tracembler – software for in silico chromosome walking in unassembled genomes.
BMC Bioinformatics 8, 151.

PBSIM 1.0.3 – PacBio Reads Simulator

PBSIM 1.0.3

:: DESCRIPTION

PacBio sequencers produced two types of characteristic reads: CCS (short and low error rate) and CLR (long and high error rate), both of which could be useful for de novo assembly of genomes. PBSIM simulates those PacBio reads by using either a model-based or sampling-based simulation.

::DEVELOPER

Yukiteru Ono ,Kiyoshi Asai ,Michiaki Hamada 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PBSIM

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Jan 1;29(1):119-21. doi: 10.1093/bioinformatics/bts649.
PBSIM: PacBio reads simulator–toward accurate genome assembly.
Ono Y, Asai K, Hamada M.

hapAssembly – Haplotype Assembly from Whole-Genome Sequence Data

hapAssembly

:: DESCRIPTION

hapAssembly  beats the previous best for the important Haplotype Assembly Problem. It is an approach to finding optimal solutions for the haplotype assembly problem under the minimum-error-correction (MEC) model.

::DEVELOPER

Chen Lab  & Lusheng Wang 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

   hapAssembly

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 15;29(16):1938-45. doi: 10.1093/bioinformatics/btt349.
Exact algorithms for haplotype assembly from whole-genome sequence data.
Chen ZZ, Deng F, Wang L.

FastMLST v0.0.15 – Multilocus Sequence Typing of draft Genome Assemblies

FastMLST v0.0.15

:: DESCRIPTION

FastMLST is a high speed standalone script wrote in Python3, which takes assemblies in FASTA format (gzipped is also allowed) and determines its ST according to MLST schemes defined in PubMLST.

::DEVELOPER

Enzo Guerrero-Araya

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

FastMLST

:: MORE INFORMATION

Citation

Guerrero-Araya E, Muñoz M, Rodríguez C, Paredes-Sabja D.
FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies.
Bioinform Biol Insights. 2021 Nov 27;15:11779322211059238. doi: 10.1177/11779322211059238. PMID: 34866905; PMCID: PMC8637782.

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.

Trinity 2.13.2 – RNA-Seq De novo Assembly

Trinity 2.13.2

:: 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

ITMO Genome Assembler 1.6.1

ITMO Genome Assembler 1.6.1

:: DESCRIPTION

ITMO Genome Assembler is a tool for de novo assembly of small and middle-sized genomes from reads, produced by Illumina/Solexa, Ion Torrent or Sanger sequencers.

::DEVELOPER

Computer Technologies Laboratory, National Research University of Information Technologies,

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • Java
:: DOWNLOAD

ITMO Genome Assembler

:: MORE INFORMATION

EvalDNA v1.1 – Evaluation of De Novo Assemblies

EvalDNA v1.1

:: DESCRIPTION

EvalDNA uses machine-learning methods to integrate genome assembly quality metrics into a single comprehensive quality score.

::DEVELOPER

Maddy MacDonald

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

EvalDNA

:: MORE INFORMATION

Citation

MacDonald ML, Lee KH.
EvalDNA: a machine learning-based tool for the comprehensive evaluation of mammalian genome assembly quality.
BMC Bioinformatics. 2021 Nov 27;22(1):570. doi: 10.1186/s12859-021-04480-2. PMID: 34837948.

MakeHub 1.0.5 – Fully Automated Generation of UCSC Assembly Hubs

MakeHub 1.0.5

:: DESCRIPTION

MakeHub is a command line tool for the fully automatic generation of of track data hubs for visualizing genomes with the UCSC genome browser. Track data hubs are data structures that contain all required information about a genome for visualizing with the UCSC genome browser.

::DEVELOPER

Bioinformatics Greifswald

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

MakeHub

:: MORE INFORMATION

Citation

Hoff KJ.
MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs.
Genomics Proteomics Bioinformatics. 2019 Oct;17(5):546-549. doi: 10.1016/j.gpb.2019.05.003. Epub 2020 Jan 28. PMID: 32001327; PMCID: PMC7056914.