This is a test version of Biostars. For the public version, visit https://www.biostars.org.
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
• 2,341 views • link
written by mschmid mschmid

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

• 0 views • link
written by 5heikki 5heikki

Thanks already helped me a lot!

• 0 views • link
written by mschmid mschmid

Log in to answer this question.

More posts like this