{"action":"closed","issue":{"url":"https://api.github.com/repos/marbl/canu/issues/66","repository_url":"https://api.github.com/repos/marbl/canu","labels_url":"https://api.github.com/repos/marbl/canu/issues/66/labels{/name}","comments_url":"https://api.github.com/repos/marbl/canu/issues/66/comments","events_url":"https://api.github.com/repos/marbl/canu/issues/66/events","html_url":"https://github.com/marbl/canu/issues/66","id":140287074,"number":66,"title":"Small plasmid lost during read correction","user":{"login":"martinghunt","id":4937411,"avatar_url":"https://avatars.githubusercontent.com/u/4937411?v=3","gravatar_id":"","url":"https://api.github.com/users/martinghunt","html_url":"https://github.com/martinghunt","followers_url":"https://api.github.com/users/martinghunt/followers","following_url":"https://api.github.com/users/martinghunt/following{/other_user}","gists_url":"https://api.github.com/users/martinghunt/gists{/gist_id}","starred_url":"https://api.github.com/users/martinghunt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/martinghunt/subscriptions","organizations_url":"https://api.github.com/users/martinghunt/orgs","repos_url":"https://api.github.com/users/martinghunt/repos","events_url":"https://api.github.com/users/martinghunt/events{/privacy}","received_events_url":"https://api.github.com/users/martinghunt/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":7,"created_at":"2016-03-11T20:42:43Z","updated_at":"2016-04-14T08:03:24Z","closed_at":"2016-04-14T08:03:24Z","body":"Here's some example PacBio data, from the NCTC sample NCTC13626...\r\n\r\nReference accession: GCA_000027045.1.\r\n\r\nFasta of reference: https://github.com/martinghunt/pacbio-14-nctc-assemblies/blob/master/NCTC13626/ref.fa\r\n\r\nFiltered subreads: ftp://ngs.sanger.ac.uk/production/pathogens/mh12/pacbio-14-nctc-assemblies/NCTC13626.filtered_subreads.fq.gz\r\n\r\nReads corrected by Canu: ftp://ngs.sanger.ac.uk/production/pathogens/mh12/pacbio-14-nctc-assemblies/NCTC13626.corrected_reads_canu_1.0.fq.gz\r\n\r\nCanu assembly: https://github.com/martinghunt/pacbio-14-nctc-assemblies/blob/master/NCTC13626/canu.1.0.fa\r\n\r\nThe plasmid that gets lost is gi|269942329|emb|FN433598.1|, which is 3kb long. I mapped the filtered subreads and the reads corrected by Canu to the whole reference with bwa mem (v0.7.12) with the option -x pacbio. It maps 259 filtered subreads to the plasmid, but no corrected reads get mapped to the plasmid (counted by running `samtools view foo.bam 'gi|269942329|emb|FN433598.1|' | wc -l`).\r\n\r\nI ran Canu version 1.0 with:\r\n\r\n    canu -p out -d canu maxThreads=8 maxMemory=16 genomeSize=3075806 -pacbio-raw filtered_subreads.fq -useGrid=0\r\n\r\nI've still got all the files and stdout/err from the run if you need anything else.\r\n\r\nMartin\r\n"}}