Tool to detect closed contigs in FASTA/FASTQ file

Question

[mschmid]

Is there a tool which can easily detect if there is is a closed contig in a FASTA/FASTQ?

Usecase is a pipeline where i assemble a lot of data with different paramters and I want to "auto detect" cases where i get closed contigs...

Writing something by myself would also be an option, but if there is something it would be nice!

[Michael]

What do you mean by closed contig?

Answer 1

[5heikki]

If you mean potentially circular contigs (overlapping 5' and 3' ends), I wrote this little script a while back. It's quite fast and works with fasta files. Note #Requires NCBI's blast+ and GNU Parallel in $PATH

Answer 2

[mschmid]

Thanks already helped me a lot!