Tag: Genome Assembly

KmerGenie 1.7051 – K-mer size Selection for Genome Assembly

KmerGenie 1.7051

:: DESCRIPTION

KmerGenie estimates the best k-mer length for genome de novo assembly. Given a set of reads, KmerGenie first computes the k-mer abundance histogram for many values of k. Then, for each value of k, it predicts the number of distinct genomic k-mers in the dataset, and returns the k-mer length which maximizes this number. Experiments show that KmerGenie’s choices lead to assemblies that are close to the best possible over all k-mer lengths.

::DEVELOPER

Rayan Chikhi, Medvedev Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • R package
  • Python

:: DOWNLOAD

 KmerGenie

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Jan 1;30(1):31-7. doi: 10.1093/bioinformatics/btt310. Epub 2013 Jun 3.
Informed and automated k-mer size selection for genome assembly.
Chikhi R1, Medvedev P.

TGNet – Visualization and Quality Assessment of de novo Genome Assemblies

TGNet

:: DESCRIPTION

TGNet is a Cytoscape-based tool for visualization and quality assessment of de novo genome assemblies. Specifically it facilitates rapid detection of inconsistencies between a genome assembly and an independently derived transcriptome assembly.

::DEVELOPER

Wurm Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java
  • Cytoscape

:: DOWNLOAD

 TGNet

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Dec 15;27(24):3425-6. doi: 10.1093/bioinformatics/btr569. Epub 2011 Oct 12.
Visualization and quality assessment of de novo genome assemblies.
Riba-Grognuz O, Keller L, Falquet L, Xenarios I, Wurm Y.

Genomix 0.2.11 – Parallel Genome Assembly using Hyracks

Genomix 0.2.11

:: DESCRIPTION

Genomix is a parallel genome assembly system built from the ground up with scalability in mind. It can assemble large and high-coverage genomes from fastq files in a short time and produces assemblies similar to Velvet or Ray in quality.

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java

:: DOWNLOAD

   Genomix

:: MORE INFORMATION

REAPR 1.0.18 – Genome Assembly Evaluation

REAPR 1.0.18

:: DESCRIPTION

REAPR (Recognising Errors in Assemblies using Paired Reads) is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls.

::DEVELOPER

REAPR  team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 REAPR

:: MORE INFORMATION

Citation:

REAPR: a universal tool for genome assembly evaluation.
Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto TD.
Genome Biol. 2013 May 27;14(5):R47

COPE 1.2.5 – Pair-end Reads Connection tool to facilitate Genome Assembly

COPE 1.2.5

:: DESCRIPTION

COPE (Connecting Overlapped Pair-End reads) is a method to align and connect the illumina sequenced Pair-End reads of which the insert size is smaller than the sum of the two read length.The connected reads can be used in genome assembly, resequencing and transcriptome research.

::DEVELOPER

COPE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 COPE

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Nov 15;28(22):2870-4. doi: 10.1093/bioinformatics/bts563. Epub 2012 Oct 8.
COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly.
Liu B, Yuan J, Yiu SM, Li Z, Xie Y, Chen Y, Shi Y, Zhang H, Li Y, Lam TW, Luo R.

fragScaff – Genome Assembly with Contiguity Preserving Transposition

fragScaff

:: DESCRIPTION

FragScaff leverages coincidences between the content of different pools as a source of contiguity information for scaffolding de novo genome assemblies. FragScaff is complementary to Lachesis, providing midrange contiguity to support robust, accurate chromosome-scale de novo genome assemblies without the need for laborious in vivo cloning steps.

::DEVELOPER

Shendure Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows
  • Perl

:: DOWNLOAD

fragScaff

:: MORE INFORMATION

Citation

Adey A, Kitzman JO, Burton JN, Daza R, Kumar A, Christiansen L, Ronaghi M, Amini S, Gunderson KL, Steemers FJ, Shendure J.
In vitro, long-range sequence information for de novo genome assembly via transposase contiguity.
Genome Res. 2014 Dec;24(12):2041-9. doi: 10.1101/gr.178319.114. Epub 2014 Oct 19. PMID: 25327137; PMCID: PMC4248320.

LACHESIS – Genome Assembly with Contact Probability Maps

LACHESIS

:: DESCRIPTION

LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly.

::DEVELOPER

Shendure Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LACHESIS

 :: MORE INFORMATION

Citation

Nat Biotechnol. 2013 Dec;31(12):1119-25. doi: 10.1038/nbt.2727. Epub 2013 Nov 3.
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions.
Burton JN1, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J.

CGAL 0.9.6b – Computing Genome Assembly Likelihoods

CGAL 0.9.6b

:: DESCRIPTION

CGAL is a tool for computing genome assembly likelihoods. It computes the likelihood of reads with respect to the assembly and a statistical model which can be used as a metric for evaluating assemblies.

::DEVELOPER

Pachter Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CGAL

:: MORE INFORMATION

Citation

Genome Biol. 2013 Jan 29;14(1):R8. [Epub ahead of print]
CGAL: computing genome assembly likelihoods.
Rahman A, Pachter L.

hapsembler 2.21 – Haplotype-specific Genome Assembly Toolkit

hapsembler 2.21

:: DESCRIPTION

Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454.

::DEVELOPER

Nilgun Donmez and Michael Brudno

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  hapsembler

:: MORE INFORMATION

Citation

Nilgun Donmez and Michael Brudno (2011)
Hapsembler: an assembler for highly polymorphic genomes.
In Proceedings of the 15th Annual international conference on Research in computational molecular biology (RECOMB’11), Springer-Verlag, Berlin, Heidelberg, 38-52.

Cortex 1.05.21 – Genome Assembly and Variation Analysis

Cortex 1.05.21

:: DESCRIPTION

Cortex is an efficient and low-memory software framework for analysis of genomes using sequence data. There are two main executables, being developed in parallel streams: cortex_con (primary contact Mario Caccamo) is for consensus genome assembly, and cortex_var (primary contact Zamin Iqbal) is for variation and population assembly.

::DEVELOPER

Cortex team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux
  • C compiler

:: DOWNLOAD

 Cortex

:: MORE INFORMATION

Citation

Nat Genet. 2012 Jan 8;44(2):226-32. doi: 10.1038/ng.1028.
De novo assembly and genotyping of variants using colored de Bruijn graphs.
Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G.