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

No

:: 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.

ntEdit v1.3.5 – Ultra Fast and Scalable Genome Assembly Polishing

ntEdit v1.3.5

:: DESCRIPTION

ntEdit is a fast and scalable genomics application for polishing genome assembly drafts and other sequences.

::DEVELOPER

BC Cancer Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ntEdit

:: MORE INFORMATION

Citation

Warren RL, Coombe L, Mohamadi H, Zhang J, Jaquish B, Isabel N, Jones SJM, Bousquet J, Bohlmann J, Birol I.
ntEdit: scalable genome sequence polishing.
Bioinformatics. 2019 Nov 1;35(21):4430-4432. doi: 10.1093/bioinformatics/btz400. PMID: 31095290; PMCID: PMC6821332.

PAVFinder v1.7.0 – Post Assembly VariantFinder

PAVFinder v1.7.0

:: DESCRIPTION

PAVFinder is a Python package that detects genomic rearrangements from whole-genome shotgun assemblies and transcriptomic events such as gene fusions, internal tandem duplications, partial tandem duplications, and novel splice variants from RNA-seq assemblies.

::DEVELOPER

BC Cancer Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

PAVFinder 

:: MORE INFORMATION

Citation

Chiu R, Nip KM, Birol I.
Fusion-Bloom: fusion detection in assembled transcriptomes.
Bioinformatics. 2020 Apr 1;36(7):2256-2257. doi: 10.1093/bioinformatics/btz902. PMID: 31790154; PMCID: PMC7141844.

Chiu R, Nip KM, Chu J, Birol I.
TAP: a targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data.
BMC Med Genomics. 2018 Sep 10;11(1):79. doi: 10.1186/s12920-018-0402-6. PMID: 30200994; PMCID: PMC6131862.

ntJoin v1.0.8 – Genome Assembly Scaffolder using minimizer Graphs

ntJoin v1.0.8

:: DESCRIPTION

ntJoin is an assembly-guided scaffolder which uses a lightweight, alignment-free mapping strategy in lieu of alignments to quickly contiguate a target assembly using one or more

::DEVELOPER

BC Cancer Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

ntJoin

:: MORE INFORMATION

Citation

Coombe L, Nikolić V, Chu J, Birol I, Warren RL.
ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs.
Bioinformatics. 2020 Jun 1;36(12):3885-3887. doi: 10.1093/bioinformatics/btaa253. PMID: 32311025; PMCID: PMC7320612.

LongStitch v1.0.1 – Correct and Scaffold Assemblies using long Reads

LongStitch v1.0.1

:: DESCRIPTION

LongStitch is a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads.

::DEVELOPER

BC Cancer Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

LongStitch

:: MORE INFORMATION

Citation

Coombe L, Li JX, Lo T, Wong J, Nikolic V, Warren RL, Birol I.
LongStitch: high-quality genome assembly correction and scaffolding using long reads.
BMC Bioinformatics. 2021 Oct 30;22(1):534. doi: 10.1186/s12859-021-04451-7. PMID: 34717540.

SAT-Assembler 20160120 – Scalable and Accurate Targeted Gene Assembly Tool

SAT-Assembler 20160120

:: DESCRIPTION

SAT-Assembler can perform targeted gene assembly for both RNA-Seq and metagenomic data. It addresses the above challenges of de novo assembly of large scale NGS data by conducting family-specic gene assembly, homology-guided overlap graph construction, and careful graph traversal.

::DEVELOPER

Dr. Yanni Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • g++ compiler

:: DOWNLOAD

 SAT-Assembler

:: MORE INFORMATION

fq2dna 21.06 – FASTQ files to de novo Assembly

fq2dna 21.06

:: DESCRIPTION

fq2dna is a command line tool to ease the de novo assembly of archaea, bacteria or virus genomes from raw high-throughput sequencing (HTS) paired-end (PE) reads.

::DEVELOPER

Alexis Criscuolo (alexis.criscuolo@pasteur.fr)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/  MacOsX

:: DOWNLOAD

fq2dna

:: MORE INFORMATION

WGA-LP – A Pipeline for Whole Genome Assembly

WGA-LP

:: DESCRIPTION

WGA-LP is a pipeline for whole genome assembly that simplifies the usage of different tools and helps the user in evaluating his results.

::DEVELOPER

WGA-LP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

WGA-LP

:: MORE INFORMATION

Citation

Rossi N, Colautti A, Iacumin L, Piazza C.
WGA-LP: a pipeline for Whole Genome Assembly of contaminated reads.
Bioinformatics. 2021 Oct 20:btab719. doi: 10.1093/bioinformatics/btab719. Epub ahead of print. PMID: 34668528.

Novo&Stitch – Genome Assembly Reconciliation tool based on Optical Map

Novo&Stitch

:: DESCRIPTION

Novo&Stitch is an assembly reconciliation tool which takes advantage of optical maps to accurately carry out assembly reconciliation.

::DEVELOPER

Weihua Pan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

Novo&Stitch

:: MORE INFORMATION

Citation

Pan W, Wanamaker SI, Ah-Fong AMV, Judelson HS, Lonardi S.
Novo&Stitch: accurate reconciliation of genome assemblies via optical maps.
Bioinformatics. 2018 Jul 1;34(13):i43-i51. doi: 10.1093/bioinformatics/bty255. PMID: 29949964; PMCID: PMC6022655.

ARBitR – Assembly Refinement with Barcode-identity-tagged Reads

ARBitR

:: DESCRIPTION

ARBitR is an overlap aware genome assembly scaffolder for linked sequencing reads.

::DEVELOPER

ARBitR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

ARBitR

:: MORE INFORMATION

Citation

Hiltunen M, Ryberg M, Johannesson H.
ARBitR: an overlap-aware genome assembly scaffolder for linked reads.
Bioinformatics. 2021 Aug 9;37(15):2203-2205. doi: 10.1093/bioinformatics/btaa975. PMID: 33216122; PMCID: PMC8352505.

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