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kapsakcj / nanoporeWorkflow

:dna: Shell scripts for working with bacterial isolate Nanopore sequence data on CDC servers
MIT License
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remove filtlong step, implement flye --asm-coverage #33

Open kapsakcj opened 3 years ago

kapsakcj commented 3 years ago

--asm-coverage 100 should allow for flye to not be overwhelmed with too much data in the initial assembly process.

https://github.com/fenderglass/Flye/blob/flye/docs/USAGE.md#reduced-contig-assembly-coverage

kapsakcj commented 3 years ago

another potential solution is to use rasusa as a tool for RANDOMLY downsampling reads instead of filtlong. It's quite fast, much faster than filtlong, and is available in a docker or singularity container