Blast many read sequences

Question

[samuel]

Hi, I have a fastq file which I think contains sequences from different organisms. Is there a way I can blast all of the sequences in the fastq file to find out where what these organisms are??

Thanks in advance.

[MSM55]

I am not able to understand what you are trying to do because your question is not explain properly but I can explain you the steps you can do.

Convert .fastq to .fasta

sed -n '1~4s/^@/>/p;2~4p' file.fq > file.fa

Use BLAST Command Line Application for fasta file

manual

[lakhujanivijay]

I have added/removed tags to keep the post relevant

Answer 1

[lakhujanivijay]

Blasting reads sounds like a bad idea considering small lengths and the number of reads. May be you can shuffle few thousand reads (seqkit?) and then try it, however, I will suggest using fastq-screen to map reads on the genomes of organims that you suspect to be present in your raw data.

[mbk0asis]

+1 for "fastq-screen"

Answer 2

[shenwei356]

You need taxonomic profiling softwares, like Kraken and Kaiju . BLAST is the slowest for this kind of task.

[lakhujanivijay]

+1 for that. That ll surely help OP