Pyramimonas orientalis virus genome, assembly pipeline

This is the pipeline for the assembly of the Pyramimonas orientalis virus genome. The raw data are available from PRJNA641252. See the paper for details.

Dependencies

• R, perl
• cutadapt
• pilon - the path $PILON_path should be specified in params.cfg
• prokka
• NCBI blast+
• bowtie2
• spades
• seqkit
• samtools
• dplyr
• tidyr
• bioformatr
• Biostrings
• IRanges
• mmgenome2
• Bio::SeqIO
• Bio::Tools::GFF

The blast+ database of SILVA_*_SSURef_tax_silva.fasta should be availbale from the path $SILVA_path specified in params.cfg.

Usage

The script assemble.sh assembles the data. Whenever data changes, the files filter_scaffolds_1.txt and filter_scaffolds_2.txt should be changed using the interactive mode of mmgenome2 (refer to filter_scaffolds.R for details).

The script finalize.sh produces the final output files and relies on the user-supplied list of selected scaffolds spades_scaffolds_selected.txt.