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).

FOCUS 1.4 – A model to Identify Organisms present in Metagenomes

FOCUS 1.4

:: DESCRIPTION

FOCUS, an innovative and agile composition based using non-negative least squares to profile and report abundant organisms present in me-tagenomic samples and their relative abundance without sequence length dependencies.

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Python

:: DOWNLOAD

 FOCUS

:: MORE INFORMATION

Citation:

Silva, G. G. Z., D. A. Cuevas, B. E. Dutilh, and R. A. Edwards, 2014
FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares.
PeerJ, 2, e425, doi:10.7717/peerj.425.

MetaCompass v2.0-beta – Reference-guided Assembly of Metagenomes

MetaCompass v2.0-beta

:: DESCRIPTION

MetaCompass represents the first effective approach for reference-guided metagenomic assembly of low-abundance bacterial genomes that can complement and improve upon de novo metagenomic assembly methods.

::DEVELOPER

Treangen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

MetaCompass

:: MORE INFORMATION

MetaCarvel v1.1 – A Scaffolder for Metagenomes

MetaCarvel v1.1

:: DESCRIPTION

MetaCarvel is an updated version of previous metagenome scaffolder Bambus 2.

::DEVELOPER

Treangen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

MetaCarvel

:: MORE INFORMATION

Citation:

Ghurye, J., Treangen, T., Fedarko, M., Hervey, W. J., & Pop, M. (2019).
MetaCarvel: linking assembly graph motifs to biological variants.
Genome biology, 20(1), 1-14.

FCMM 2.0.0 – Functional Characterization of Multiple Metagenome samples

FCMM 2.0.0

:: DESCRIPTION

FCMM is a pipeline for top-k based functional characterization of multiple metagenome samples to infer the major functions as well as their quantitative scores in a comparative metagenomics manner.

::DEVELOPER

the Bioinformatics Laboratory,Konkuk University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • awk (GNU awk 3.1.7)
  • sed (GNU sed 4.2.1)
  • BWA (v0.7.10)
  • DIAMOND (v0.7.8.57)
  • Trimmomatic (v0.33)

:: DOWNLOAD

 FCMM

:: MORE INFORMATION

Citation

FCMM: A comparative metagenomic approach for functional characterization of multiple metagenome samples.
Lee J, Lee HT, Hong WY, Jang E, Kim J.
J Microbiol Methods. 2015 Aug;115:121-8. doi: 10.1016/j.mimet.2015.05.023

MEGAN 6.18.0 – Metagenome analysis

MEGAN 6.18.0

:: DESCRIPTION

MEGAN (MEta Genome ANalyzer) allows laptop analysis of large metagenomic data sets. In a preprocessing step, the set of DNA sequences is compared against databases of known sequences using BLAST or another comparison tool. MEGAN is then used to compute and explore the taxonomical content of the data set, employing the NCBI taxonomy to summarize and order the results. A simple lowest common ancestor algorithm assigns reads to taxa such that the taxonomical level of the assigned taxon reflects the level of conservation of the sequence. The software allows large data sets to be dissected without the need for assembly or the targeting of specific phylogenetic markers. It provides graphical and statistical output for comparing different data sets.

::DEVELOPER

the Algorithms in Bioinformatics lab.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

 MEGAN

:: MORE INFORMATION

Citation

Analysis of 16S rRNA environmental sequences using MEGAN.
Mitra S, Stärk M, Huson DH.
BMC Genomics. 2011 Nov 30;12 Suppl 3:S17. doi: 10.1186/1471-2164-12-S3-S17.

PHYLOSHOP 1.01 – Predicts 16S rRNA Gene Fragments in Metagenomes

PHYLOSHOP 1.01

:: DESCRIPTION

PHYLOSHOP is a pipeline that predicts 16S rRNA gene fragments in metagenomes, reports the taxonomic assignment of these fragments, and visualizes their taxonomy distribution.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 PHYLOSHOP

:: MORE INFORMATION

Citation:

Neethu Shah, Haixu Tang, Thomas G. Doak and Yuzhen Ye.
Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics.
Pac Symp Biocomput. p:165-76 (2011)

MetaTISA – Translation Initiation Site Annotation for Metagenomes

MetaTISA

:: DESCRIPTION

MetaTISA is tool with an aim to improve translationa initiation sites (TISs) prediction of current gene-finders for metagenomes. The method employs a two-step strategy to predict TISs by first clustering metagenomic fragments into phylogenetic groups and then predicting TISs independently for each group in an unsupervised manner. As evaluated on experimentally verified TISs, MetaTISA greatly improves the accuracies of TIS prediction of current gene-finders.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 MetaTISA

:: MORE INFORMATION

Citation

Gang-Qing Hu, Jiang-Tao Guo, Yong-Chu Liu, and Huaiqiu Zhu.
MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction.
Bioinformatics 2009,25(14):1843-1845.

PyroTrimmer 1.1 – Preprocessor of Metagenome Sequences

PyroTrimmer 1.1

:: DESCRIPTION

PyroTrimmer is a program that trims barcodes, linkers, primers, and sequence region with low quality scores from 454 sequence reads.

::DEVELOPER

PyroTrimmer team

:: SCREENSHOTS

PyroTrimmer

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 PyroTrimmer

:: MORE INFORMATION

Citation

J Microbiol. 2012 Oct;50(5):766-9. doi: 10.1007/s12275-012-2494-6.
PyroTrimmer: a software with GUI for pre-processing 454 amplicon sequences.
Oh J1, Kim BK, Cho WS, Hong SG, Kim KM.