Hello Jennifer:

Good news! the ONT data assembles into 37 pieces (N50=308 kbp), of which one appears to be a probable plasmid (scaffold31 len=16939 in the fasta file named below). 
This is a good result despite the read length distribution of the ONT data being on the short side (median=453 bp), making the assembly challenging.

I have placed the raw uncorrected fastq read data (1D/2D) and 2 best assemblies here:

ftp://ftp.bcgsc.ca/supplementary/JG20160707/

A summary of the ONT reads is available (summary.xls)

Assembly stats here:

ftp://ftp.bcgsc.ca/supplementary/JG20170209/README.txt

We have tried a variety of assemblers and are sharing the best ones (assemblies of the recent SJ_42 sample sequence data and one from combining with the data from last year's run SJ_16). 

We also looked at the synteny to the recently sequenced M. chimaera MC045 (https://www.ncbi.nlm.nih.gov/nucleotide/1129842099?report=genbank&log$=nuclalign&blast_rank=1&RID=9T6E9UJH014)
and the genome structure of one of our best ONT-only assembly (./wga/canu/SJ42/canu-allONT_LINKS_sj42_1D2D_passfail.scaffolds.fa) is consistent with it -- see attached.

In the coming weeks, we will further refine the genome draft by MiSeq-correction of ONT reads, draft polishing, further scaffolding and automated gap-closing.

Let us know if you need additional data. We are also available to discuss by phone/in person.

Best,
Rene

===========
Rene Warren
BC Cancer Agency, Genome Sciences Centre
570 W 7th Ave #100, Vancouver, BC V5Z 4S6
(604) 707-5900 #673235


Assemblies of Mycobacterium chimaera ONT sequence data*

sample		n	n:500	n:N50	min	N80	N50	N20	E-size	max	sum	software	filename
SJ42+MiSeq	5935	2595	276	500	2202	6443	21626	12233	57396	8636396	SPADES  	NA
SJ42    	69	69	13	1871	65967	143563	249152	180658	514695	5862275	canu    	SJ_42.1D2D.passfail.contigs.fasta	
SJ42   	  	37	37	7	1871	183809	308324	517927	328123	625539	5862275	canu+LINKS 	canu-allONT_LINKS_sj42_1D2D_passfail.scaffolds.fa
SJ16+SJ42	71     	71      12      1474    60617   150795  297028  185781  517026  5891171 canu    	ntm.contigs.fasta    
SJ16+SJ42	38     	38      5       1474    148765  372033  1210043 507648  1210043 5891171 canu+LINKS  	canu-allONT_LINKS_sj16-sj42.scaffolds.fa


*Note: miniasm assemblies of yielded no contigs