assemble 3 SRA files for a single species

Question

[Sillpositive]

Hello everyone,

I have one species with 3 SRA file SRR3571227.sra SRR3571228.sra SRR3571228.sra. I want to convert to a FASTQ file with SRAToolkit but it's very unclear for me.. before I have to first assemble the 3 SRA files and make one SRA file or it is not necessary?

[h.mon]

You should convert each file separately.

Answer 1

[ATpoint]

My suggestion:

## 1. Use fastq-dump on each of the files, e.g. parallelized with GNU parallel:
ls *.sra | parallel "fastq-dump --gzip --split-3 {}"

## 2. Check files with fastqc:
ls *.fastq.gz | parallel "fastqc {}"

## 3. If metrics are ok, combine them:
cat SRR*_1.fastq.gz > merged_1.fastq.gz
cat SRR*_2.fastq.gz > merged_2.fastq.gz

## 4. (optional): Trim with skewer for adapters and low-quality bases/reads:
skewer -n -q 25 -Q 25 -m pe merged_1.fastq.gz merged_2.fastq.gz

## 5. Proceed with your downstream alignment or assembly