search

bhattlab / bhattlab_workflows

Computational workflows for metagenomics tasks, by the Bhatt lab
http://www.bhattlab.com
46 stars 15 forks source link

Spades often gets stuck on read error correction #24

Open bsiranosian opened 5 years ago

bsiranosian commented 5 years ago

This happens in about 5% of cases, looping away and wasting compute with no error. See https://github.com/ablab/spades/issues/152

A solution is to split the read correction and assembler, and skip the read correction if it fails to compete after some reasonable amount of time. spades-hammer can be run alone, then spades with the --only-assembler option