Filtering phage contigs

Post assembly a contigs.fasta file will be produced. After mapping reads to all these contigs it should be possible to determine if complete assembly of the phage genome has occurred. If there is a single contig with higher coverage than all other contigs, this suggests this has occured and is a good sign.

To extract the largest contig or contigs above a certain length you can use the script like this

 perl ~/Documents/scritps/ --file input.fasta --len 10000 

This will produced a new file called input_gt10000.fasta that contains all contigs greater than 10000 bp in length.

To extract contigs by name then you can use this script

perl ~/Documents/scripts/ --file contigs.fasta --name NODE_1_ 

This will extract the contig named “>NODE_1_length_92674_cov_68.7486_ID_277” from contigs.fasta and save it to a file called NODE_1_.fasta.