Short read Illumina genome pipe

• QC of raw reads
• Short read assmembly
• Genome Annotation
• Species identification on reads(NCBI_taxon)
• AMR detection on assembly with CARD
• Plasmid detection on assembly plasmidfinder

Dependencies:

• snakemake
• unicycler
• fastp
• kraken2
• abricate
• prokka
• ideel
• diamond
• krona

Setup databases

abricate --setupdb
abricate --check
prokka --setupdb
prokka --listdb  

kraken2-build --download-library bacteria --threads 100 --db NCBI_bac_tax

diamond makedb --in uniprot.faa -d diamond_uniprot_db --threads 100

in config.json you can change path to your database

{
	"md": "normal",
	"db1": "/path_to/NCBI_bac_tax",
	"db2": "/path_to/diamond_uniprot_db",
	"threads": 100
}

check pipe

Clone the repo.

Put your Illumina data in folder reads/ inside of repo and name them like this.

Illumina reads: TP1234_R1.fastq.bz2 and TP1234_R2.fastq.bz2

in config.json you can change the mode of the assemblie with the 3 possible modes (see more info Unicycler).

conservative
normal = Default
bold

snakemake --configfile config.json --forceall --dag | dot -Tpdf > dag.pdf

run pipe

cd ...Illumina_genome_pipe/
snakemake --configfile config.json --cores 100

Enjoy the results in /results

Troubleshooting

If prokka gets error blastASN reinstall it:

conda install prokka --force --yes

If unicycler failes at spades downgrade it:

conda install spades=3.11.0 --force --yes