Spherical – An iterative approach for Large Metagenome Assemblies

Spherical

:: DESCRIPTION

Spherical is an iterative approach to assembling metagenomic datasets. Spherical has been designed to produce a more complete assembly from deep sequenced metagenomic data.

::DEVELOPER

The Creevey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Spherical

:: MORE INFORMATION

Citation

Hitch, Thomas CA, and Christopher J. Creevey.
Spherical: an iterative workflow for assembling metagenomic datasets.
BMC bioinformatics 19.1 (2018): 20.”

crAss v2.2 – Cross-Assembly of Metagenomes

crAss v2.2

:: DESCRIPTION

crAss is a web tool for comparative metagenomics using cross-assembly.

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux /
  • Perl

:: DOWNLOAD

crAss

:: MORE INFORMATION

Citation:

Reference-independent comparative metagenomics using cross-assembly: crAss
Bas E. Dutilh, Robert Schmieder, Jim Nulton, Ben Felts, Peter Salamon, Robert A. Edwards and John L. Mokili
Bioinformatics 28: 3225-3231 (2012).

Scaffold_builder v2.2 – Order Contigs generated by draft sequencing along a Reference Sequence

Scaffold_builder v2.2

:: DESCRIPTION

Scaffold_builder is software to order contigs generated by draft sequencing along a reference sequence. Gaps are filled with N’s and small overlaps are aligned with Muscle and the consensus created with IUPAC codes. Scaffold_builder can help in the assembly and annotation of genomes by revealing what is missing and allowing targeted sequencing to close those gaps.

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Scaffold_builder

:: MORE INFORMATION

Citation

Source Code Biol Med. 2013 Nov 22;8(1):23. doi: 10.1186/1751-0473-8-23.
Combining de novo and reference-guided assembly with scaffold_builder.
Silva GG1, Dutilh BE, Matthews TD, Elkins K, Schmieder R, Dinsdale EA, Edwards RA.

SWALO – Scaffolding with Assembly Likelihood Optimization

SWALO

:: DESCRIPTION

SWALO is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing.

::DEVELOPER

Pachter Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  •  Bowtie 2

:: DOWNLOAD

SWALO

:: MORE INFORMATION

 

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.

AssemblX – Toolkit for Rapid and Reliable Multi-Gene Assemblies

AssemblX

:: DESCRIPTION

AssemblX toolkit allows the assembly of up to 25 transcriptional units, consisting of many more individual DNA fragments, on a single plasmid in the host Saccharomyces cerevisiae.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res, 45 (10), e80 2017 Jun 2
AssemblX: A User-Friendly Toolkit for Rapid and Reliable Multi-Gene Assemblies
Lena Hochrein , Fabian Machens , Juergen Gremmels , Karina Schulz , Katrin Messerschmidt , Bernd Mueller-Roebe

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.

scarpa 0.241 – Scaffolding Reads with Practical Algorithms

scarpa 0.241

:: DESCRIPTION

Scarpa is a stand-alone scaffolding tool for NGS data. It can be used together with virtually any genome assembler and any NGS read mapper that supports SAM format. Other features include support for multiple libraries and an option to estimate insert size distributions from data.

::DEVELOPER

Nilgun Donmez and Michael Brudno

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 scarpa

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 15;29(4):428-34. doi: 10.1093/bioinformatics/bts716. Epub 2012 Dec 29.
SCARPA: scaffolding reads with practical algorithms.
Donmez N, Brudno M.

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.

treecat – Phylogenetic Comparative Assembly

treecat

:: DESCRIPTION

treecat (phylogenetic tree based contig arrangement tool) takes several genomes and their relationships in a phylogenetic tree into account to estimate a possible ordering of the contigs.

::DEVELOPER

treecat team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

treecat

:: MORE INFORMATION

Citation

Husemann, P. & Stoye, J.
Phylogenetic comparative assembly
Algorithms for Molecular Biology, 2010, Vol. 5(1), pp. 3