I decided to release a minor hotfix to MaSuRCA 3.2.9 on 11/20/2019 keeping version number the same, but with a small change: now the final output file final.genome.scf.fasta contains scaffolds. Previous version split scaffolds and output contigs in that file. To recover the scaffolds from 3.2.8 assemblies you can run:
<MaSuRCA path>/bin/recover_scaffolds.pl < final.genome.scf.fasta >final.genome.scf.scaffolds.fasta
The NA12878 assembly of newly basecalled release3+4 Nanopore+Illumina data (see previous posts) now has the following statistics (N50 computed with 3.1Gbp human genome size):
Total sequence: 2,886,141,146
Number of scaffolds: 3,240
Longest scaffold: 56,745,809
Scaffold N50: 14,764,183
Scaffold L50: 63
Number of contigs: 3,448
Longest contig: 51,762,539
Contig N50: 9,580,052
Contig L50: 88
<MaSuRCA path>/bin/recover_scaffolds.pl < final.genome.scf.fasta >final.genome.scf.scaffolds.fasta
The NA12878 assembly of newly basecalled release3+4 Nanopore+Illumina data (see previous posts) now has the following statistics (N50 computed with 3.1Gbp human genome size):
Total sequence: 2,886,141,146
Number of scaffolds: 3,240
Longest scaffold: 56,745,809
Scaffold N50: 14,764,183
Scaffold L50: 63
Number of contigs: 3,448
Longest contig: 51,762,539
Contig N50: 9,580,052
Contig L50: 88
The assembly is posted here:
ftp://ftp.ccb.jhu.edu/pub/alekseyz/na12878/na12878_MaSuRCA_3.2.8_nanopore_wgs_consortium_37x_GIAB_100x.scaffolds.fa
The consensus quality stats:
Substitution Errors: 49,520
Insertion/Deletion Errors: 115,752
Consensus Quality: 99.9943 (or 0.4 errors per 10000 bases)
The consensus quality stats:
Substitution Errors: 49,520
Insertion/Deletion Errors: 115,752
Consensus Quality: 99.9943 (or 0.4 errors per 10000 bases)
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