02_READ_BASED_ANNOTATION

PhyloFlash is a method to identify and assemble full-length SSU sequences from reads. Please see the sub-coassemblies protocol for details on that

1. Kraken2 profiling of contigs

# Using a file containing all of the contigs from all samples as input:

kraken2 merged.contigs.fa --db standardKraken2 --threads 40 > merged.contigs.kraken2.output

# When this finishes, you have your taxa assignments for each contig. 
# Now we can recruit reads from all samples to our merged contigs database we made for mapping.

2. Kraken2 profiling of reads

# Perhaps more importantly, kraken2 takes reads as input. With reads info we can 
# easily figure out how many of each taxa are present. The former method takes a bit more matching.