Construction of JVD and JMAG

This is a repository for the codes used in the Tomofuji et al (prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features associated with diets, populations, and diseases).
Our scripts recover
・Metagenome assembled genomes (MAGs)
・CRISPR spacers on the MAGs
・Viral genomes
from the metagenome shotgun sequencing data.
Scripts related to the analysis performed in the Tomofuji et al are also deposited.

Please also see our GitHub repository (https://github.com/ytomofuji/JMAG_JVD)

We also deposited three multiple sequence alignment (MSA) files which were used for the construction of the phylogenetic trees. These MSA files were used as inputs for iqtree.
crAss_TerL.msa・・・MSA file for the TerL gene of the crAss-like phages
JMAG_BAC.msa・・・MSA file for the bacterial marker genes of the JMAG representative genomes
Nori.msa・・・MSA file for the beta-porphyranase and related genes

Contact: Yoshihiko Tomofuji: ytomofuji_at_sg.med.osaka-u.ac.jp