MATAM 1.6.0 – Mapping-Assisted Targeted-Assembly for Metagenomics

MATAM 1.6.0

:: DESCRIPTION

MATAM is a software dedicated to the fast and accurate targeted assembly of short reads sequenced from a genomic marker of interest. It has been applied to the assembly of 16S rRNA markers and is validated on simulated, synthetic and genuine metagenomes.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MATAM

:: MORE INFORMATION

Citation:

Pericard P, Dufresne Y, Couderc L, Blanquart S, Touzet H.
MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes.
Bioinformatics. 2018 Feb 15;34(4):585-591. doi: 10.1093/bioinformatics/btx644. PMID: 29040406.

ELOPER 1.2 – Elongation of Paired-end Reads for de novo Assembly

ELOPER 1.2

:: DESCRIPTION

ELOPER is a pre-processing tool for pair-end sequences that produces a better read library for assembly programs.

::DEVELOPER

YanaiLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Perl / C++ Compiler

:: DOWNLOAD

 ELOPER

:: MORE INFORMATION

Citation:

ELOPER: elongation of paired-end reads as a pre-processing tool for improved de novo genome assembly.
Silver DH, Ben-Elazar S, Bogoslavsky A, Yanai I.
Bioinformatics. 2013 Jun 1;29(11):1455-7. doi: 10.1093/bioinformatics/btt169.

ConPADE 1.00 – Contig Ploidy and Allele Dosage Estimation

ConPADE 1.00

:: DESCRIPTION

ConPADE is a tool used to estimate contig ploidy and allele dosage in polyploid genome assemblies.

::DEVELOPER

Microsoft Computational Biology Tools

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ConPADE

:: MORE INFORMATION

Citation

Margarido GR, Heckerman D.
ConPADE: genome assembly ploidy estimation from next-generation sequencing data.
PLoS Comput Biol. 2015 Apr 16;11(4):e1004229. doi: 10.1371/journal.pcbi.1004229. PMID: 25880203; PMCID: PMC4400156.

MetaVelvet 1.2.01 / MetaVelvet-SL – An Extension of Velvet Assembler to de novo Metagenomic Assembly / utilizing Supervised Learning

MetaVelvet 1.2.01 / MetaVelvet-SL

:: DESCRIPTION

MetaVelvet is an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

MetaVelvet-SL is an extension of Velvet assembler to de novo metagenomic assembler utilizing supervised learning

::DEVELOPER

Sakakibara Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MetaVelvet/ MetaVelvet-SL 

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Nov 1;40(20):e155. doi: 10.1093/nar/gks678. Epub 2012 Jul 19.
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads.
Namiki T1, Hachiya T, Tanaka H, Sakakibara Y.

Fermi 1.1 – WGS de novo Assembler based on the FMD-index for large Genomes

Fermi 1.1

:: DESCRIPTION

Fermi is a de novo assembler for Illumina reads from whole-genome short-gun sequencing. It also provides tools for error correction, sequence-to-read alignment and comparison between read sets. It uses the FMD-index, a novel compressed data structure, as the key data representation.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Fermi

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Jul 15;28(14):1838-44. doi: 10.1093/bioinformatics/bts280. Epub 2012 May 7.
Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly.
Li H.

HapCompass 0.8.2 – A Cycle-Basis Algorithm for Accurate Haplotype Assembly

HapCompass 0.8.2

:: DESCRIPTION

HapCompass for polyploid genomes can currently be used to create accurate pairwise SNP phasings.Given a set of aligned sequence reads in a SAM file and a set of variant calls in VCF format, HAPCOMPASS will assemble reads into haplotypes.

::DEVELOPER

The Istrail Laboratory of Brown University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 HapCompass

:: MORE INFORMATION

Citation

HapCompass: a fast cycle basis algorithm for accurate haplotype assembly of sequence data.
Aguiar D, Istrail S.
J Comput Biol. 2012 Jun;19(6):577-90. doi: 10.1089/cmb.2012.0084.

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.

Tedna 1.3 – Transposable Element De Novo Assembler

Tedna 1.3

:: DESCRIPTION

Tedna is a lightweight de novo transposable element assembler. It assembles the transposable elements directly from the raw reads.

::DEVELOPER

INRA, URGI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 Tedna

:: MORE INFORMATION

Citation

Tedna: a Transposable Element De Novo Assembler.
Zytnicki M, Akhunov E, Quesneville H.
Bioinformatics. 2014 Jun 3. pii: btu365.

TCGA-Assembler 2.0.6 – Open-Source Software for Retrieving and Processing TCGA Data

TCGA-Assembler 2.0.6

:: DESCRIPTION

TCGA-Assembler is an open-source, freely available tool that automatically downloads, assembles, and processes public The Cancer Genome Atlas (TCGA) data, to facilitate downstream data analysis by relieving investigators from the burdens of data preparation.

::DEVELOPER

Yuan Ji Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package

:: DOWNLOAD

 TCGA-Assembler

 :: MORE INFORMATION

Citation

TCGA-Assembler: Open-Source Software for Retrieving and Processing TCGA Data
Yitan Zhu, Peng Qiu, Yuan Ji*
Nat Methods. 2014 Jun;11(6):599-600. doi: 10.1038/nmeth.2956.

MEGAHIT v1.2.9 – Large and Complex Metagenomics Assembly via Succinct de Bruijn graph

MEGAHIT v1.2.9

:: DESCRIPTION

MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.

::DEVELOPER

Dinghua Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python
  • G++

:: DOWNLOAD

 MEGAHIT

:: MORE INFORMATION

Citation

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
Li D, Liu CM, Luo R, Sadakane K, Lam TW.
Bioinformatics. 2015 Jan 20. pii: btv033.