Genome Sequencing and Assembly of SJ42
using Illumina MiSeq and Ox. Nanopore Tech. long reads
March 15th, 2017

n	n:500	L50	min	N80	N50	N20	E-size	max	sum	name
43	33	4	747	209932	570557	940706	579669	1099614	5944060	unicycler.fasta
43	33	4	747	209973	570557	940761	579679	1099614	5944164	unicycler_polish_out.fasta
37	27	3	747	240706	640788	1693028	932964	1693028	5944164	links.unicycler_polish_out.fasta
37	27	3	747	240706	640788	1693028	932964	1693028	5944164	sealer.links.unicycler_polish_out.fasta
1	1	1	5868151	5868151	5868151	5868151	5868151	5868151	5868151	SJ42_ragoutMC045.fa
22	12	2	747	13458	16585	33560	21096	33560	76013	SJ42_ragoutUNPLACED.fa

The M. chimaera SJ42 genome was constructed
with unicycler, a hybrid ONT+Illumina assembler (unicycler.fasta)
and polished with those same data (refer to the unicycler documentation on the polishing steps) (unicycler_polish_out.fasta)
The resulting assembly was re-scaffolded with LINKS using ONT-only data, and made 6 merges (links.unicycler_polish_out.fasta)
Scaffold merges were consistent with the MC045 chromosome structure. The merges resulted in 6 predicted overlaps. 
The automated gap-filling software sealer closed 2 out of these 6 overlaps. 

The reference-based scaffolder ragout was used, in conjunction with the reference M. chimaera MC045 chromosome, to generate a possible chromosome sequence for SJ42 (SJ42_ragoutMC045.fa). Because MC045 plasmids were not used in the ragout scaffolding process, unplaced SJ42 sequences represent possible plasmid sequences (SJ42_ragoutUNPLACED.fa).


### Software Resources:
--------------

Unicycler
https://github.com/rrwick/Unicycler

LINKS
http://www.bcgsc.ca/platform/bioinfo/software/links

Sealer
http://www.bcgsc.ca/platform/bioinfo/software/sealer

Ragout
https://github.com/fenderglass/Ragout