Invertebrate

Create a directory named INVERTEBRATE_GENOME_REFERENCES/ and go inside it.

[Whole Genome] (ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/invertebrate/)

1. Create a directory INVERTEBRATE_GENOME_REFERENCES/WG/ and go inside it.

2. Download the assembly summary file, with a list of all the virus sequences included.

   curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/invertebrate/assembly_summary.txt' > assembly_summary_invertebrate.txt

3. Get a list of complete and latest sequences.

   awk -F "\t" '{print $1,$20}' assembly_summary_invertebrate.txt > ftpdirpaths_complete_latest.txt

4. Download the fasta sequences.

   cat ftpdirpaths_complete_latest.txt | while read line; do dir='echo $line | cut -d " " -f 1 ';mkdir -p $dir;url='echo $line | cut -d " " -f 2';echo "wget -P $dir $url/*" ; done >> wget_all_invertebrate.sh (creates download script)

   bash REFERENCES/INVERTEBRATE_GENOME_REFERENCE/WG/wget_all_invertebrate.sh (executes download script)

   WARNING! This step will create a folder per genome and download several files into it, including nucleotide and protein sequences. Before executing this command please make sure you have sufficient storage space. We advise you create a new directory and execute this command from inside it, that will keep your working space well organized. In this example we have created the folder all_genomes for the download.

5. Create the multifasta file with the genomic data.

   find REFERENCES/PROTOZOO_GENOME_REFERENCE/WG/all_genomes ! -name '*from_genomic.fna.gz' -name '*_genomic.fna.gz' -exec zcat {} \; > WG/invertebrate_wg_all.fna

6. Get length of each sequence

   samtools faidx REFERENCES/INVERTEBRATE_GENOME_REFERENCE/WG/invertebrate_wg_all.fna (generates index: invertebrate_wg_all.fna.fai)

   cut -f1-2 REFERENCES/INVERTEBRATE_GENOME_REFERENCE/WG/invertebrate_wg_all.fna.fai > REFERENCES/INVERTEBRATE_GENOME_REFERENCE/WG/genome_length.txt

7. Create Bowtie2 genome index

`bowtie2-build REFERENCES/INVERTEBRATE_GENOME_REFERENCE/WG/invertebrate_wg_all.fna REFERENCES/INVERTEBRATE_GENOME_REFERENCE/WG/bwt2/invertebrate_all`

9. Create BLAST files - BLASTn

`makeblastdb -in REFERENCES/INVERTEBRATE_GENOME_REFERENCE/WG/invertebrate_wg_all.fna -parse_seqids -dbtype nucl -out REFERENCES/INVERTEBRATE_GENOME_REFERENCE/BLAST/blastn/INVERTEBRATE_blastn`