I'm using SPAdes to do de novo transcriptome assembly using RNA-seq (from Illumina). However, the new version SPAdes 3.14.1 has excluded the read error correction step for RNA-seq. So I want to use the BayesHammer which comes with SPAdes to do the error correction. However, I can't find the usage of BayesHammer. I want to ask if this can be used as a standalone tool for RNA-seq. Any one please can you give me any instructions. Thanks a lot.
I'd suggest simply using rCorrector instead of manually trying BayesHammer.
The program is also part of the Oyster River Protocol and is recommended to be used prior to de novo transcriptome assembly.
rCorrector can simply be installed in a conda environment.
If you really want to use BayesHammer as you are used to, you should be able to install it together with an older version of SPAdes (3.11.1 as one of the authors recommends here).
Hope that helps.