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Tool to detect closed contigs in FASTA/FASTQ file

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!

contig assambly close
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written by mschmid 18

What do you mean by closed contig?

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written by Michael Dondrup 5.6K

2 answers

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

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written by 5heikki 1.1K

Thanks already helped me a lot!

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written by mschmid 18

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