New software/tool of possible interest:
Source: MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples
Software: http://segatalab.cibio.unitn.it/tools/metamlst/
Abstract:
Metagenomic characterization of microbial communities has the potential to become a tool to identify pathogens in human samples. However, software tools able to extract strain-level typing information from metagenomic data are needed. Low-throughput molecular typing schema such as Multilocus Sequence Typing (MLST) are still widely used and provide a wealth of strain-level information that is currently not exploited by metagenomic methods. We introduce MetaMLST, a software tool that reconstructs the MLST loci of microorganisms present in microbial communities from metagenomic data. Tested on synthetic and spiked-in real metagenomes, the pipeline was able to reconstruct the MLST sequences with >98.5% accuracy at coverages as low as 1×. On real samples, the pipeline showed higher sensitivity than assembly-based approaches and it proved successful in identifying strains in epidemic outbreaks as well as in intestinal, skin and gastrointestinal microbiome samples.
Citation: Zolfo, M., Tett, A., Jousson, O., Donati, C., & Segata, N. (2016). MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples. Nucleic Acids Research, gkw837.