thackl / cr-genomes

Supplementary code and data for genomes of C.roenbergensis: E4-10P, BVI, Cflag and RCC970-E3

Generic scripts used in data analysis

https://github.com/thackl/sam-scripts

• bam-coverage
• bam-junctions

https://github.com/thackl/seq-scripts

• seq-circ-restart
• seq-circ-trim
• seq-comp

https://github.com/thackl/phylo-scripts

• tax-resolve

Kmer-based genome size estimation for strain E4-10P

genome-size-estimation/genome-size-estimation.R

C. roenbergensis draft assemblies

Assemblies have been processed with redundans, but still contain bacterial contaminations and potential misassemblies, and are unpolished.

file	assembler	primary_data	num_seqs	sum_len	min_len	max_len	N50
CrBV-c0b.fa	Canu 1.8	pacbio	343	39107625	5118	1533637	429009
CrBV-c1b.fa	Canu 1.8	pacbio	394	40117058	5308	975077	270687
CrBV-f1b.fa	Flye 2.3.7	pacbio	213	37884398	5129	1475468	479063
CrBV-w5b.fa	Wtdbg 2.1	pacbio	268	38356196	5098	1458748	435830
CrCf-c0b.fa	Canu 1.8	pacbio	272	34561700	5589	1022239	229877
CrCf-c1b.fa	Canu 1.8	pacbio	311	36551481	5490	1011470	270089
CrCf-f1b.fa	Flye 2.3.7	pacbio	216	34137805	5245	946461	276367
CrCf-w5b.fa	Wtdbg 2.1	pacbio	187	33253511	5670	938012	321504
CrEa-c0b.fa	Canu 1.8	pacbio	265	35731872	5057	1514847	402275
CrEa-c1b.fa	Canu 1.8	pacbio	293	36283366	5128	1087465	282182
CrEa-f1b.fa	Flye 2.3.7	pacbio	190	34509388	5337	1335512	348875
CrEa-gen-dp-4.5.fa	SPAdes 3.6.1	miseq + corr. pacbio	315	29710364	1002	910477	228292
CrEa-w5b.fa	Wtdbg 2.1	pacbio	376	36791972	5002	1475054	432668
CrEa-w6b.fa	Wtdbg 2.1	pacbio	371	36429848	5057	947144	405606
CrEa-w7b.fa	Wtdbg 2.1	pacbio	333	36790428	5080	1467234	546423
CrEa-w8b.fa	Wtdbg 2.1	pacbio	385	36725772	5002	1259187	383112
CrRC-c0b.fa	Canu 1.8	pacbio	513	30455408	5151	563941	99385
CrRC-c1b.fa	Canu 1.8	pacbio	392	34047446	6587	635481	155376
CrRC-f1b.fa	Flye 2.3.7	pacbio	396	33792790	5193	720955	131225
CrRC-w5b.fa	Wtdbg 2.1	pacbio	296	31845612	5053	701287	178453