Tag: Metagenomic Analysis

Parallel-META 3.6 – A Parallel Metagenomic Analysis Pipeline

Parallel-META 3.6

:: DESCRIPTION

Parallel-META is a GPGPU and Multi-Core CPU based software which can parallelly analyze massive metagenomic data structures, report the classification, construction and distribution on phylogenetic & taxonomic and functional level.

::DEVELOPER

Bioinformatics Group , Single-cell Reseearch Center of Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences (QIBEBT-CAS).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs
  • C Compiler
  • R

:: DOWNLOAD

 Parallel-META

:: MORE INFORMATION

Citation

Parallel-META 2.0: enhanced metagenomic data analysis with functional annotation, high performance computing and advanced visualization.
Su X, Pan W, Song B, Xu J, Ning K.
PLoS One. 2014 Mar 3;9(3):e89323. doi: 10.1371/journal.pone.0089323.

Parallel-META: efficient metagenomic data analysis based on high-performance computation.
Su X, Xu J, Ning K.
BMC Syst Biol. 2012 Jul 16;6 Suppl 1:S16. doi: 10.1186/1752-0509-6-S1-S16.

SIGMA 1.0.2 – Strain-level Identification of Genomes from Metagenomic Analysis for Biosurveillance

SIGMA 1.0.2

:: DESCRIPTION

SIGMA is a novel sequence similarity-based approach for strain-level identification of genomes from metagenomic analysis for biosurveillance.

::DEVELOPER

the Pan lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 SIGMA

:: MORE INFORMATION

Citation

Sigma: Strain-level Inference of Genomes from Metagenomic Analysis for Biosurveillance.
Ahn TH, Chai J, Pan C.
Bioinformatics. 2014 Sep 29. pii: btu641

PALEOMIX 1.3.2 – Characterization of Ancient and Modern Genomes by SNP Detection and Phylogenomic and Metagenomic analysis

PALEOMIX 1.3.2

:: DESCRIPTION

The PALEOMIX pipeline is a user-friendly package designed for Unix-like systems and largely automates the analyses related to whole genome re-sequencing. It is compatible with a full range of sequence data and performs a series of user-defined analyses, including read trimming, collapsing of overlapping mate-pairs, read mapping, PCR duplicate removal, SNP calling, and metagenomic profiling.

::DEVELOPER

The Centre for Anthropobiology and Genomics of Toulouse

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PALEOMIX

:: MORE INFORMATION

Citation

Nat Protoc. 2014 May;9(5):1056-82. doi: 10.1038/nprot.2014.063. Epub 2014 Apr 10.
Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX.
Schubert M1, Ermini L1, Der Sarkissian C1, Jónsson H1, Ginolhac A1, Schaefer R2, Martin MD1, Fernández R1, Kircher M3, McCue M4, Willerslev E1, Orlando L1.

SmashCommunity 1.6p2 – Metagenomic Analysis and Annotation Tool

SmashCommunity 1.6p2

:: DESCRIPTION

 SmashCommunity is a stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. It comes with built-in support for state-of-the-art software for essential metagenomic tasks such as assembly and gene prediction, and can be easily extended to support additional software. SmashCommunity provides tools to estimate the quantitative phylogenetic and functional compositions of metagenomes, compare compositions of multiple metagenomes and produce intuitive visual representations of such analyses.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SmashCommunity

:: MORE INFORMATION

Citation

Arumugam, M., Harrington, E. D., Foerstner, K. U., Raes, J. and P. Bork. (2010)
SmashCommunity: A metagenomic annotation and analysis tool,
Bioinformatics, 26, 2977-8.