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Shamir-Lab / Recycler

This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir
BSD 3-Clause "New" or "Revised" License
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No output produced #41

Open sum732 opened 4 years ago

sum732 commented 4 years ago

I have got the recent pull of Recycler installed. The contigs/scaffolds were produced by SPAdes-3.11.1. The kmer size etc were all under 55 etc. Recycler is NOT generating any outputs. The BAM file was produced as per the tutorial.

Any ideas what could be the issues? I am have got about 7 contigs from the assembly ( SPAdes) >500bp ( largest is about 1500bp). Simply mapping these contigs to a reference via BLAST, I have got a really good score and %identity. Also the edges do overlaps. However, no output from Recycler.

dpellow commented 4 years ago

Thanks for your interest in using Recycler. Does the Recycler run complete without producing output or is it getting stuck during the run? If there are many short contigs besides the 7 long ones you mentioned, Recycler could just be taking a long time to complete running. Recycler will only assemble plasmids from overlapping contigs that form a circular path and have mostly uniform coverage. If this is not the case in your data then Recycler will not assemble plasmids. Otherwise, we can help you to debug if you can send us more details of the dataset. Hope that helps!

sum732 commented 4 years ago

Thank you for the quick response. Recycler does complete the run and finishes with no output. From "SPAdes" there are short contigs as well. Here is what is shown on STDERR:

(7.5625, 430.5257300917254, 1336.0)                                                             
================== path, coverage levels when added ====================                        
(4936, ' nodes remain in component\n')                                                          
==================final_paths identities after updates: ================

And then empty output is produced. For this plasmid in total there are about 70K PE reads. About the uniform coverage, that needs to be checked. Can you recommend parameters that I should try? I have changed the kmer etc with no affects. Can you recommend any other tools that you think may be useful if coverage is the issue?

dpellow commented 4 years ago

I can try to help you with this - send me an email at dpellow@post.tau.ac.il and I'll see what I can do.