Running rounds of ntLink
Support for automated running of iterations or rounds ntLink was introduced in v1.3.0. Running additional rounds of ntLink can lead to a final assembly with improved contiguity metrics. To reduce runtime of the ntLink rounds and avoid re-mapping reads, we use liftover code to liftover mapping coordinates from one round to the next.
Example results from running additional rounds of ntLink scaffolding on two human (individual NA24385) assemblies: a short read assembly from ABySS and a long read assembly from Shasta.
Additional iterations of ntLink can be launched using the ntLink_rounds makefile. The run_rounds_gapfill target additionally runs gap-filling at each iteration, while the run_rounds target does not.
For example, to run 5 rounds of ntLink:
ntLink_rounds run_rounds target=my_assembly.fa reads=long_reads.fq.gz k=24 w=250 rounds=5