Main tool : sylph
Full documentation: https://github.com/bluenote-1577/sylph/wiki
sylph is a program that can perform ultrafast (1) ANI querying or (2) metagenomic profiling for metagenomic shotgun samples.
# all fasta -> one *.syldb; fasta are assumed to be genomes
sylph sketch genome1.fa genome2.fa -o database
#EQUIVALENT: sylph sketch -g genome1.fa genome2.fa -o database
# multi-sample sketching of paired reads
sylph sketch -1 A_1.fq B_1.fq -2 A_2.fq B_2.fq -d output_read_sketch_folder
# multi-sample sketching for single end reads, fastq are assumed to be reads
sylph sketch reads.fq
#EQUIVALENT: sylph sketch -r reads.fq
# ANI querying
sylph query database.syldb *.sylsp -t (threads) > ani_queries.tsv
# taxonomic profiling
sylph profile database.syldb *.sylsp -t (threads) > profiling.tsv