search

kango2 / ausarg

This repository contains information and code for AusARG genome assemblies.
0 stars 0 forks source link

Launch new tool "GreenHill" on Bassiana and Tiliqua #18

Closed kiratalreja3 closed 1 year ago

kiratalreja3 commented 1 year ago

Juicer alternative : https://github.com/ShunOuchi/GreenHill

kiratalreja3 commented 1 year ago

Tool unlikely to work well since people reported days and weeks of runtime for 1GB genomes. Testing with 24 hour wall time.

kiratalreja3 commented 1 year ago

Bassiana Results :

Screenshot 2023-09-28 at 9 28 06 am

Much better results than Juicer+3D-DNA, although with gaps (which juicer added as well). Investigating further. Greenhill has support to use long read data for better performance, trying that.

kiratalreja3 commented 1 year ago

Generating .HiC and .Assembly file to give the assembly to AutoHic and Juicer for visualisation

kiratalreja3 commented 1 year ago
Screenshot 2023-09-29 at 10 31 43 am

GreenHill assembly HiC map

kiratalreja3 commented 1 year ago

AutoHiC did not work/make any changes in the assembly.

kiratalreja3 commented 1 year ago

Ran GreenHill in long-read mode, with PacBio and ONT data - but that resulted in a more fragmented assembly. Will have to investigate further. Closing this for now.