Playground.md

Some datasets:

ID	Taxonomy
GCF_000006945.2	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
GCF_009831375.1	Mediterraneibacter gnavus ATCC 29149
GCF_020526745.2	Escherichia coli g83
GCF_900476435.1	Shewanella benthica
NC_012920_1_HsMT	Homo sapiens (Mitoch)
NC_020014_1_NcCHL	Nannochloropsis gaditana (Chloroplast)

Chopping reads

Using seqfu shred we can chop a sequence in fragments, in a systematic and ordered manner:

fu-shred -l 100 -s 5 -o PREFIX INPUT_FASTA.fa

Files

In the NBI cluster, you can find genomes, reads and kraken2, metaphlan4, humann3 profiling:

/qib/platforms/Informatics/outgoing/workshops/biobakery/playground/

This directory contains:

• data: input FASTA files (genomes)
• simulation: systematic fragments (FASTQ)
• kraken2: profiling of both reads and genomes using the "Standard" database
• bracken: recalibrated Kraken
• metaphlan4
• humann_3.7