Metabin

Description

metabin website

For comprehensive taxonomic binning, we developed the ‘MetaBin’ web server and standalone program for faster and more accurate taxonomic assignment of single and paired-end sequence reads of varying lengths (≥45 bp) obtained from both Sanger and next-generation sequencing platforms. We benchmarked it using both simulated reads (> 1 million) and real metagenomic datasets. MetaBin correctly assigns a higher number of reads to their expected taxonomic lineages with a lower error frequency as compared to other methods. It displays high accuracy (positive predictive value (PPV) ≥99%) along with high sensitivity (≥94%) for various read lengths. In particular, for short Illumina reads (~45-75 bp) it makes about 4% more assignments as compared to its closest competitors with near 100% accuracy when reference genomes are available.

Environment Modules

Run module spider metabin to find out what environment modules are available for this application.

Environment Variables

• HPC_METABIN_DIR - installation directory
• HPC_METABIN_BIN - executable directory

Additional Usage Information

Metabin uses Jim Kent's Blat application as an alignment method that is much faster than Blastx. Unfortunately, Blat has a bug which causes it to crash with large reference databases, like nr (see the Blat Wiki Page). As a workaround, we suggest dividing large reference databases into multiple files. To implement this, it is necessary to run the prepareinput step of Metabin with the -b n option, and run the Blat analyses separately.

Citation

If you publish research that uses metabin you have to cite it as follows:

Sharma, V.K., Kumar, N., Prakash, T., Taylor, T.D., 2012. Fast and Accurate Taxonomic Assignments of Metagenomic Sequences Using MetaBin. PLoS One 7.

Categories

genomics