Automatic SRA data processing on IIITD HPC

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:

1. Only download SRA dataset in .sra format

2. Get final paired/unpaired fastq files corresponding to the SRA dataset

3. Download reference Genome and the corresponding annotations

4. Download the Indexes

5. Get the BAM file corresponding to alignment

6. Get sorted BAM file

7. Get count matrix

Some of the open source packages that we used for processing SRA data - SAMtools, fasterqdump, SRAtoolkit, Trimmomatic, Hisat2, MultiQC, Entrez, sortmerna, BS4, pysradb.