CLIOR v1 – Higher Recall in Metagenomic Sequence Classification Exploiting Overlapping Reads

CLIOR v1

:: DESCRIPTION

CLIOR (CLassification Improvement with Overlapping Reads) is a metagenomic classification method that exploits the information captured by the reads overlap graph of the input dataset in order to improve recall and f-measure.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CLIOR

:: MORE INFORMATION

Citation

BMC Genomics, 18 (Suppl 10), 917 2017 Dec 6
Higher Recall in Metagenomic Sequence Classification Exploiting Overlapping Reads
Samuele Girotto , Matteo Comin , Cinzia Pizzi

MetaPhyler 1.25 – Taxonomic Profiling for Metagenomic Sequences

MetaPhyler 1.25

:: DESCRIPTION

MetaPhyler is a novel taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference. Our classifier, based on BLAST, uses different thresholds (automatically learned from the reference database) for each combination of taxonomic rank, reference gene, and sequence length. Our reference database includes marker genes from all complete genomes, several draft genomes and the NCBI nr protein database. Results on simulated metagenomic datasets demonstrate that MetaPhyler outperforms previous tools used in this context (CARMA, MEGAN and PhymmBL).

::DEVELOPER

Bo Liu 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MetaPhyler

:: MORE INFORMATION

Citation:

BMC Genomics. 2011;12 Suppl 2:S4. Epub 2011 Jul 27.
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences.
Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M.

MetaBinG 0.4 / MetaBinG2 – ultra-fast Metagenomic Sequence Classification system using GPUs

MetaBinG 0.4 / MetaBinG2

:: DESCRIPTION

MetaBinG  is an ultra-fast metagenomic sequence classification system using graphic processing units (GPUs).

MetaBinG2 is a fast and accurate metagenomic sequence classification system for samples with many unknown organisms

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MetaBinG / MetaBinG2

:: MORE INFORMATION

Citation:

Biol Direct. 2018 Aug 22;13(1):15. doi: 10.1186/s13062-018-0220-y.
MetaBinG2: a fast and accurate metagenomic sequence classification system for samples with many unknown organisms.
Qiao Y, Jia B, Hu Z, Sun C, Xiang Y, Wei C.

PLoS One. 2011;6(11):e25353. doi: 10.1371/journal.pone.0025353. Epub 2011 Nov 23.
MetaBinG: using GPUs to accelerate metagenomic sequence classification.
Jia P1, Xuan L, Liu L, Wei C.

integron_gene_fetch 1.0 – Discovery of Chromosomal Integrons from Metagenomic Sequences

integron_gene_fetch 1.0

:: DESCRIPTION

integron_gene_fetch is developed to get integron genes from metagenomic sequencing reads. It is capable of getting the integron mobile genes more efficiently, as these genes are extremely difficult to be detected in whole-genome assembly.  By assembling the dataset and traces all potential paths between any two contigs that consist of recombination sites, the integron_gene_fetch tool is able to get more integron genes given a pre-determined set of recombination site sequences.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

   integron_gene_fetch

:: MORE INFORMATION

Citation

Yu-Wei Wu, Mina Rho, Thomas G. Doak and Yuzhen Ye.
Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes.
Appl. Environ. Microbiol. August 2012 vol. 78 no. 15 5288-5296

AbundanceBin 1.0.1 – Abundance-based tool for Binning Metagenomic Sequences

AbundanceBin 1.0.1

:: DESCRIPTION

AbundanceBin is an abundance-based tool for binning metagenomic sequences, such that the reads classified in a bin belong to species of identical or very similar abundances. AbundanceBin also gives estimations of species abundances and their genome sizes—-two important characteristic parameters for a microbial community.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 AbundanceBin

:: MORE INFORMATION

Citation:

Yu-Wei Wu and Yuzhen Ye.
A novel abundance-based algorithm for binning metagenomic sequences using l-tuples.
Lecture Notes in Computer Science2010, Volume 6044/2010, 535-549 (RECOMB 2010)

MetaBin 1.0 – Comprehensive Taxonomic Assignments of Metagenomic Sequences

MetaBin 1.0

:: DESCRIPTION

MetaBin is a program for accurate, fast and highly sensitive taxonomic assignments of metagenomic sequences

::DEVELOPER

Laboratory for Integrated Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

 MetaBin

:: MORE INFORMATION

Citation

Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin.
Sharma VK, Kumar N, Prakash T, Taylor TD.
PLoS One. 2012;7(4):e34030. doi: 10.1371/journal.pone.0034030.

MaxBin 2.2 – Binning Assembled Metagenomic Sequences

MaxBin 2.2

:: DESCRIPTION

MaxBin is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.

::DEVELOPER

The Joint BioEnergy Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MaxBin

:: MORE INFORMATION

Citation

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets.
Wu YW, Simmons BA, Singer SW.
Bioinformatics. 2015 Oct 29. pii: btv638.

Centrifuge 1.0.1-beta – Classifier for Metagenomic Sequences

Centrifuge 1.0.1-beta

:: DESCRIPTION

Centrifuge is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 Centrifuge

:: MORE INFORMATION

MetaCompass 1.0 – Comparative Assembly of Metagenomic Sequences

MetaCompass 1.0

:: DESCRIPTION

MetaCompass is a software package for comparative assembly of metagenomic reads. MetaCompass achieves comparable assembly performance to the state of the art de novo assemblers, but these two different approaches complement each other a lot. So combining contigs between MetaCompass and other independent de novo assemblers give us the best overall metagenomic assembly.

::DEVELOPER

Bo Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • BLAST
  • Bowtie 2
  • Perl

:: DOWNLOAD

 MetaCompass

:: MORE INFORMATION