IHM-DB: a curated collection of metagenomics data from the Indian Himalayan Region, and automated pipeline for 16S rRNA amplicon-based analysis (AutoQii2)

Database (Oxford). 2023 Jun 2;2023:baad039. doi: 10.1093/database/baad039.

ABSTRACT

Indian Himalayan metagenome database (IHM-DB) is a web-based database consisting of information on metagenomic datasets from various databases and publications that are specifically reported from the Indian Himalayan Region (IHR). The online interface allows users to view or download the dataset-specific information for the respective states, category-wise, or according to the hypervariable region. The IHM-DB also provides an opportunity for the users to access the metagenomic publications from the IHR as well as upload their microbiome information to the website. Additionally, an open-source 16S rRNA amplicon-based automated bioinformatics pipeline, AutoQii2, allows users to analyze the single-end and paired-end raw reads. AutoQii2 provides an automated approach for performing analysis such as quality check, adapter and chimera removal and exploits the latest ribosomal database project classifier for taxonomic assignments. The source code of the AutoQii2 pipeline is available at https://gitlab.com/khatriabhi2319/autoqii2. Database URL https://ham.ihbt.res.in/ihmdb and https://fgcsl.ihbt.res.in/ihmdb.

PMID:37279783 | PMC:PMC10243898 | DOI:10.1093/database/baad039