Automatic SRA data processing on IIITD HPC
Downloading and processing SRA data is a mess, but it doesn't have to be!
Downloading and processing SRA data is a mess, but it doesn't have to be!
Enter GEO ID
Enter GEO ID
Enter Options
Enter Options
Enter SSH credentials
Enter SSH credentials
Our pipeline allows a user to automate the downloading and processing of SRA data on their confifured HPC using a mobile app.
Our pipeline allows a user to automate the downloading and processing of SRA data on their confifured HPC using a mobile app.
We provide the following options to the user:
We provide the following options to the user:
Only download SRA dataset in .sra format
Get final paired/unpaired fastq files corresponding to the SRA dataset
Download reference Genome and the corresponding annotations
Download the Indexes
Get the BAM file corresponding to alignment
Get sorted BAM file
Get count matrix
Our Workflow
Our Workflow
Some of the open source packages that we used for processing SRA data - SAMtools, fasterqdump, SRAtoolkit, Trimmomatic, Hisat2, MultiQC, Entrez, sortmerna, BS4, pysradb.
Some of the open source packages that we used for processing SRA data - SAMtools, fasterqdump, SRAtoolkit, Trimmomatic, Hisat2, MultiQC, Entrez, sortmerna, BS4, pysradb.
Check out the GitHub repositories
Check out the GitHub repositories
