Database Help

Home page of IHM-DB has seven navigation bar including current number of datasets counter which are divided into three section State-wise, Category-wise and Hypervariable-wise Home page provides an overview to the IHM-DB . It contains a navigation bar with seven tabs namely Home, Browse, User-tutorials, Publications, Download, Data-Submit and Search. A background image describes the Indian Himalayas with a snow line range, including green Dhauladhar mountains of Himachal Pradesh. The database also contains the current counts of datasets obtained from NCBI, MG-RAST, and EMBL databases, respectively, for every IHR state, category and hypervariable regions.

Explanation of dataset: user can view datasets of NCBI, MGRAST and EMBL databases of a selected State by users and filter dataset by using Data Filtering section

Search Criteria

AutoQii2 Pipeline Help

A user-friendly computational automated workflow, ‘AutoQii2’ is also presented for analyzing 16S amplicon-based datasets. AutoQii2 is primarily designed for eliminating multi-step analysis involved in analyzing single-end or paired-end reads using Quantitative Insights into Microbial Ecology (QIIME) 2. QIIME 2 is a command-line Interface (CLI) that requires a significant number of commands for data processing, and many times the analysis must be repeated for desirable results, which can make the analysis difficult and error-prone. AutoQii2 pipeline uses an automated interface where users are only required to enter needful parameters for repeated analysis. AutoQii2 uses popular fastQC, cutadapt, and QIIME 2 platforms for performing the quality check, adapter and chimera removal, operational taxonomic units (OTUs) identification, and taxonomic assignments. Moreover, the users can access all the output results in a dedicated folder for their convenience. AutoQii2 also provides the users an interface where the qiime2 view result files can be automatically viewed in the browser without the use of a command. This developed workflow provides a fully automated and faster data analysis where bulk datasets can be analyzed in a short time.

Source code of developed pipeline is Publically available at GitLab Platform, For more information and usage click on Gitlab =>

Download NCBI data Using Fastq-dump

Fastq-dump is a tool for downloading sequencing reads from NCBI’s Sequence Read Archive (SRA). These sequence reads will be downloaded as FASTQ files. How these FASTQ files are formatted depends on the fastq-dump options used.

Install

How to download ? Example with Environmental Dataset:

Other Links:

SRA Toolkit Documentation: fastq-dump

sra-tools

parallel-fastq-dump