I ran Quast to compare all of our current Olympia oyster genome assemblies.

See Jupyter Notebook in Results section for Quast execution.

Results:

Output folder: http://ift.tt/2mL6aX9

Heatmapped table of results: http://ift.tt/2rg0UPE

Very enlightening!

After all the difficulties with PB Jelly, it has produced the most large contigs. However, it does also have the highest quantity and rate of N’s of all the assemblies produced to date.

BEST OF:

contigs (>= 50000 bp): pbjelly_sjw_01 (894)

Largest Contig: redundans_sjw_02 (322,397bp)
Total Length: pbjelly_sjw_01 (1,180,563,613bp)
Total Length (>=50,000bp): pbjelly_sjw_01 (57,741,906bp)
N50: redundans_sjw_03 (17,679bp)

Jupyter Notebook (GitHub): 20180116_swoose_oly_assembly_comparisons_quast.ipynb

                <script>
                jQuery(function($){
                    var target_height = $(window).height();
                    $("iframe.iframe-class").height(target_height);
                });
                </script>

from Sam’s Notebook http://ift.tt/2rcMboZ

Assembly Comparisons – Oly Assemblies Using Quast
Tagged on: