Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

MCP Database Indexing, Read Mapping, and Community Profiling

DP Donovan H. Parks
FR Fabio Rigato
PV Patricia Vera-Wolf
LK Lutz Krause
PH Philip Hugenholtz
GT Gene W. Tyson
DW David L. A. Wood
request Request a Protocol
ask Ask a question
Favorite

Microba Community Profiler is propriety software available by contacting Microba Life Sciences at https://microba.com/microbiome-research. MCP is a whole-genome alignment tool, which uses a combination of BWA v0.7.17 (Li and Durbin, 2009), SAMtools v1.7 (Li et al., 2009), and custom software optimized to ensure that reads are assigned to reference genomes that are closely related to the strains comprising a metagenomic sample. Mapping the 140 in silico mock communities (each 2.1 Gb, 2 × 150 bp paired-end reads) required 37.6 ± 9.9 min on average and profiling required 14.5 ± 2.4 min on average when using 64 Intel Xeon 2.00 GHz processors.

Copyright and License information:  ©2021 Parks, Rigato, Vera-Wolf, Krause, Hugenholtz, Tyson and Wood.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

0/150

tip Tips for asking effective questions

+ Description

Write a detailed description. Include all information that will help others answer your question including experimental processes, conditions, and relevant images.

post Post a Question
0 Q&A