How to assemble mulitple paired-end files?

Question

[A_heath]

Hi all,

I downloaded multiple paired-end reads from the SRA (NCBI) and I want to assemble two paired-end read files with each other. All the files look like this:

SRRXXX_1.fastq

SRRXXX_2.fastq

SRRYYY_1.fastq

SRRYYY_2.fastq

SRRWWW_1.fastq

SRRWWW_2.fastq

First, I use Megahit to do so, is that appropriate for what I want to do?

Then, I tried this:

for file in *.fastq;

do

f=$(basename $file)

megahit -1 "$file"_1.fastq -2 "$file"_2.fastq -o "$file"_assembled.fasta/;

done;

But it didn't work because the file names aren't correct and it makes sense because _1.fastq or _2.fastq are added to the original file names. Unfortunately, I don't know how to proceed differently ...

How could I assemble both paired-end read files at the same time and do this for all files?

Thank you for your help, it will be greatly appreciated!

[GenoMax]

I want to assemble two paired-end read files with each other.

I don't know what exactly you mean by that. If you are looking to merge R1/R2 reads because they overlap (e.g. size of insert is smaller than length of sequencing) then you need to be using a program like bbmerge.sh from BBMap suite or FLASH. If you want to actually assemble the sequences into contigs then megahit would be appropriate.

Answer 1

[Assa Yeroslaviz]

this should work

for file in *_1.fastq;

do

f=$(echo $file | sed -E "s/\_.*//");

megahit -1 "$f"_1.fastq -2 "$f"_2.fastq -o "$file"_assembled.fasta/; 
done

[A_heath]

Yes!! Perfect, it works great! Thank you so much for your help Assa Yeroslaviz.