Consensus A corrected & synchronized:
nanopore reads
canu assembly with 1/2 downsized filtered long reads
mapped with illumina:spades_carefull assembled contigs
end repeats corrected to circularize sequence
coordinates origin synchronized with White & al. sequence
id origin size (nt)
new nomenclature, CDS corrected
> DRors consensus A corrected & synchronized (Chromosome 1) 2644252
> DRAors consensus A corrected & synchronized (Chromosome 2) 412139
> DRBors consensus A corrected & synchronized (plasmid MP1) 177323
> DrCors consensus A corrected & synchronized (plasmid CP1) 45508
> DRors Chromosome 1 CDS
> DRAors Chromosome 2 CDS
> DRBors plasmid MP1 CDS
> DRCors plasmid CP1 CDS
> Consensus A gff
> Genes cross-match: D.rad R1 genes from White et al. (1999) , Hua et al. (2016) , Consensus A corrected (2020). Gene by gene blastp comparison of all 3 sequences
> Dra self match / excel format
Consensus A: nanopore reads / canu assembly with 1/2 downsized filtered long reads / mapped with illumina:spades_carefull assembled contigs
id origin size (nt)
> atig00000001 consensus A (Chromosome 1) 2729484
> atig00000272 consensus A (Chromosome 2) 492405
> atig00000273 consensus A (plasmid MP1) 278796
> atig00000306 consensus A (plasmid CP1) 83601
> Consensus A gff
number of contigs: 4
total contigs length: 3584286
mean contig size: 896071.50
median contig size: 492405
longest contig: 2729484
shortest contig: 83601
contigs > 500 nt: 4 (100.00 %)
contigs > 1K nt: 4 (100.00 %)
contigs > 10K nt: 4 (100.00 %)
contigs > 100K nt: 3 (75.00 %)
contigs > 1M nt: 1 (25.00 %)
N50: 2729484
L50: 1
N80: 492405
L80: 2
Consensus B: nanopore reads / canu assembly with 1/2 downsized filtered long reads / mapped with illumina:megahit assembled contigs
id origin size (nt)
> btig00000001 consensus B (Chromosome 1) 2729460
> btig00000272 consensus B (Chromosome 2) 492445
> btig00000273 consensus B (plasmid MP1) 278815
> btig00000306 consensus B (plasmid CP1) 83601
> Consensus B gff
number of contigs: 4
total contigs length: 3584321
mean contig size: 896080.25
median contig size: 492445
longest contig: 2729460
shortest contig: 83601
contigs > 500 nt: 4 (100.00 %
contigs > 1K nt: 4 (100.00 %
contigs > 10K nt: 4 (100.00 %
contigs > 100K nt: 3 (75.00 %)
contigs > 1M nt: 1 (25.00 %)
N50: 2729460
L50: 1
N80: 492445
L80: 2
Genes cross match (uncorrected version)
> Genes cross-match: D.rad R1 genes from White et al. (1999) , Hua et al. (2016) , Consensus A & B (2020). Gene by gene blastp comparison of all 4 sequences
> Replicons synteny: D.rad R1 genes from white et al. (1999) , Hua et al. (2016) , Consensus A & B (2020) full-scale replicon genes blastp comparison
> Dra self match / excel format
Questions, comments & bug reports to : yvan.zivanovic@u-psud.fr |
