Tag: Assembly

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.

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

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.

SvABA 1.1.0 – Structural Variation and Indel Detection by local Assembly

SvABA 1.1.0

:: DESCRIPTION

SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly.

::DEVELOPER

Jeremiah Wala (jwala@broadinstitute.org) — Rameen Berkoukhim lab — Dana Farber Cancer Institute, Boston, MA.

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SvABA

:: MORE INFORMATION

Citation

Wala JA, Bandopadhayay P, Greenwald NF, O’Rourke R, Sharpe T, Stewart C, Schumacher S, Li Y, Weischenfeldt J, Yao X, Nusbaum C, Campbell P, Getz G, Meyerson M, Zhang CZ, Imielinski M, Beroukhim R.
SvABA: genome-wide detection of structural variants and indels by local assembly.
Genome Res. 2018 Apr;28(4):581-591. doi: 10.1101/gr.221028.117. Epub 2018 Mar 13. PMID: 29535149; PMCID: PMC5880247.

EWRA – Edge-Weighted Reconstruction integrating aDNA Assembly graph

EWRA

:: DESCRIPTION

The EWRA algorithm computes a parsimonious reconstruction of marker adjacencies minimizing the Single-Cut-or-Join (SCJ) distance along a given phylogenetic tree, including the information provided by an assembly graph of ancient DNA (aDNA) data at one internal node of the tree.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

EWRA

:: MORE INFORMATION

Citation

Luhmann N, Chauve C, Stoye J, Wittler R.
Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework.
IEEE/ACM Trans Comput Biol Bioinform. 2018 Nov-Dec;15(6):2094-2100. doi: 10.1007/978-3-319-12418-6_17. Epub 2018 Mar 15. PMID: 29993816.

HASLR – Fast Hybrid Assembly of Long Reads

HASLR

:: DESCRIPTION

HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

HASLR

:: MORE INFORMATION

Citation

Haghshenas E, Asghari H, Stoye J, Chauve C, Hach F.
HASLR: Fast Hybrid Assembly of Long Reads.
iScience. 2020 Aug 21;23(8):101389. doi: 10.1016/j.isci.2020.101389. Epub 2020 Jul 25. PMID: 32781410; PMCID: PMC7419660.

SALSA v2.3 – Scaffold long read Assemblies with Hi-C data

SALSA v2.3

:: DESCRIPTION

SALSA is a tool to scaffold long read assemblies with Hi-C.

::DEVELOPER

MarBL (Maryland Bioinformatics Labs)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SALSA

:: MORE INFORMATION

Citation

Ghurye J, Pop M, Koren S, Bickhart D, Chin CS.
Scaffolding of long read assemblies using long range contact information.
BMC Genomics. 2017 Jul 12;18(1):527. doi: 10.1186/s12864-017-3879-z. PMID: 28701198; PMCID: PMC5508778.

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.