add_accession_contigs_megahit_dir: Function to concatenate megahit final contigs into one fasta...

In uashogeschoolutrecht/structural_colours: Package For Project Structural Colour

Description

Function to concatenate megahit final contigs into one fasta file with sample accession added to the headers. This function can be used to create one file for input in makeblastdb to create a blast database of all the final contigs.

Usage

add_accession_contigs_megahit_dir(megahit_dir, outfile)

Arguments

megahit_dir	String, path to directorty in which the fastq files are present, here the blast and contigs folder will be made.
outfile	String, path to output file to create.

Value

This functions creates the output file specified, containing the sequencing in fasta format.

Examples

## Not run: 
add_accession_contigs_megahit(megahit_dir = "/home/$USER/research_drive/geodescent/samples/MGYS00000974/megahit",
                              outfile = "/home/$USER/research_drive/geodescent/samples/MGYS00000974/blast/contigs/all_samples2.fa")
                              
## End(Not run)

uashogeschoolutrecht/structural_colours documentation built on June 20, 2020, 4:07 p.m.