dsurujon / genome-assembly

genome assembly for strep pneumo main scripts

genome-assembly

genome assembly for Streptococcus pneumoniae

Usage

Use this script to assemble complete genomes from a collection of contigs (e.g. obtained from Illumina sequencing)

assemble_genome.py -i [inputfile] -l [logfile]

The output will be an unannotated fasta file with the complete genomic sequence.

The output can then be sent to RAST for annotation.

Genome Statistics

Use the genome_stats.py script to generate a summary of key features of a genome file. This is usually useful once a newly assembled genome has been annotated

genome_stats.py -i [inputfile] -g [genome format] -o [outputfile]

use either gbk or fasta as the genome format.

Genome Statistics HTML

This is an updated version of genome_stats.py that generates an HTML file that contains more detailed summary statistics including histograms of gene/CDS/RNA feature lengths.

genome_stats_html.py -i [inputfile] -g [genome format] -o [output directory] -f [output HTML file]

The output directory will contain all necessary files for the html file to display properly.