additions to materials

[tavareshugo]

In rough order of priority:

• [x] Use SNP-sites to extract variants from the panaroo alignment (with the -C option to count the number of invariant sites). Then run IQ-Tree with -fconst parameter using the previous number. (see below)
• [x] To assess assembly quality use bandage (can load graph file from flye) - nice assembly should have few unresolved bubbles in the graph.
• [ ] Modify assembly script to include some read filtering (e.g. filtlong or nanoq).
• [ ] Include FastQC step beforehand?

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Code for extracting SNPs and running IQ-TREE:

# Extract variant sites
snp-sites core_gene_alignment.aln -o core_gene_alignment_snps.aln

# Extract count of invariant sites
snp-sites -C core_gene_alignment.aln > constant_sites.txt

# fancier
iqtree -fconst $(cat constant_sites.txt) -s core_gene_alignment_snps.aln -nt AUTO -ntmax 8 -mem 8G -bb 1000 -m MFP

# manually add those numbers
iqtree -fconst 123,123,123,123 -s core_gene_alignment_snps.aln -nt AUTO -ntmax 8 -mem 8G -bb 1000 -m MFP

[tavareshugo]

Link to slides: https://docs.google.com/presentation/d/1ENJiefOD_wHsQOlzLuiRiZ6N_2kPoNpUSCxplt2asgQ/edit?usp=sharing

[tavareshugo]

Will not incorporate these, as they will become obsolete if we eventually switch to https://github.com/avantonder/assembleBAC-ONT