CAT/BAT v5.2.3 – Taxonomic Classification of Contigs and Metagenome-assembled Genomes

CAT/BAT v5.2.3

:: DESCRIPTION

Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies.

::DEVELOPER

Bas E. Dutilh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

CAT/BAT

:: MORE INFORMATION

Citation

von Meijenfeldt FAB, Arkhipova K, Cambuy DD, Coutinho FH, Dutilh BE.
Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT.
Genome Biol. 2019 Oct 22;20(1):217. doi: 10.1186/s13059-019-1817-x. PMID: 31640809; PMCID: PMC6805573.

CrossClassify – Mapping between different Taxonomic Classifications

CrossClassify

:: DESCRIPTION

CrossClassify is a tool for mapping different metagenomic analyses on a common taxonomic classification

::DEVELOPER

the Algorithms in Bioinformatics lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

CrossClassify

:: MORE INFORMATION

Citation

Balvočiūtė M, Huson DH.
SILVA, RDP, Greengenes, NCBI and OTT – how do these taxonomies compare?
BMC Genomics. 2017 Mar 14;18(Suppl 2):114. doi: 10.1186/s12864-017-3501-4. PMID: 28361695; PMCID: PMC5374703.

16S classifier – Fast and Accurate Taxonomic Classification of 16S rRNA Sequences

16S classifier

:: DESCRIPTION

16S Classifier‘ is a Random Forest based tool which is developed to carry out fast, efficient and accurate taxonomic classification of 16S rRNA sequences. It has the unique ability to classify small Hypervariable Regions of 16S rRNA.

::DEVELOPER

MetaBioSys laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 16S classifier

:: MORE INFORMATION

Citation

16S classifier: a tool for fast and accurate taxonomic classification of 16S rRNA hypervariable regions in metagenomic datasets.
Chaudhary N, Sharma AK, Agarwal P, Gupta A, Sharma VK.
PLoS One. 2015 Feb 3;10(2):e0116106. doi: 10.1371/journal.pone.0116106.

SPANNER 1.0.0 – Homology-based Taxonomic Classification of Protein Sequences

SPANNER 1.0.0

:: DESCRIPTION

SPANNER (Simularity Profile ANNotatER) extends LCA to perform supervised homology-based taxonomic classification of metagenomic fragments.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX
  • C++ Compiler
  • Python

:: DOWNLOAD

 SPANNER

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 1;29(15):1858-64. doi: 10.1093/bioinformatics/btt313.
SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles.
Porter MS, Beiko RG.