cjfields
commented
3 years ago We will have a separate QC workflow for these steps.
Open cjfields opened 3 years ago
cjfields
commented
3 years ago We will have a separate QC workflow for these steps.
Most assemblies have metrics similar to this one:
---------------- Information for assembly 'NA19028.final.megahit_results/final.contigs.fa' ---------------- Number of scaffolds 119 Total size of scaffolds 91508 Longest scaffold 4962 Shortest scaffold 310 Number of scaffolds > 1K nt 22 18.5% Number of scaffolds > 10K nt 0 0.0% Number of scaffolds > 100K nt 0 0.0% Number of scaffolds > 1M nt 0 0.0% Number of scaffolds > 10M nt 0 0.0% Mean scaffold size 769 Median scaffold size 601 N50 scaffold length 747 L50 scaffold count 34 scaffold %A 29.98 scaffold %C 20.00 scaffold %G 20.43 scaffold %T 29.59 scaffold %N 0.00 scaffold %non-ACGTN 0.00 Number of scaffold non-ACGTN nt 0 Percentage of assembly in scaffolded contigs 0.0% Percentage of assembly in unscaffolded contigs 100.0% Average number of contigs per scaffold 1.0 Average length of break (>25 Ns) between contigs in scaffold 0 Number of contigs 119 Number of contigs in scaffolds 0 Number of contigs not in scaffolds 119 Total size of contigs 91508 Longest contig 4962 Shortest contig 310 Number of contigs > 1K nt 22 18.5% Number of contigs > 10K nt 0 0.0% Number of contigs > 100K nt 0 0.0% Number of contigs > 1M nt 0 0.0% Number of contigs > 10M nt 0 0.0% Mean contig size 769 Median contig size 601 N50 contig length 747 L50 contig count 34 contig %A 29.98 contig %C 20.00 contig %G 20.43 contig %T 29.59 contig %N 0.00 contig %non-ACGTN 0.00 Number of contig non-ACGTN nt 0I still see some scaffolds that could be removed because they are artifacts like this one with low complexity sequences: