shandley/hecatomb

Long reads support

owenkuo-TW opened this issue · 5 comments

owenkuo-TW commented

Hi,

Already complete the test. But failed with path to pacbio hifi.fastq.gz and also a tsv noted sample/file path. Would encounter error like below "Error in rule pool_paired_unmapped_R2: jobid: 9". Please kindly provide option to proceed. Thanks!

beardymcjohnface commented

Hi, sorry it might not be that obvious. Run Hecatomb like so:
hecatomb run --trim filtlong ...
I would probably also use --assembly cross if you dont have too many samples, but for hifi reads you might want to try an assembler and parameters better tuned for hifi reads.

owenkuo-TW commented

Thanks for the reply. Can I apply contigs to conduct partial hecatmob pipeline?

beardymcjohnface commented

Sure! If you just want the read-annotations without the assembly, just add 'read_annotations' to specify the target output files:
hecatomb run read_annotations ...

owenkuo-TW commented

Thanks for the reply! Just complete the read_annotations option, but can I apply assembled contigs into hecatomb process?

beardymcjohnface commented

Not easily. It would probably be easier to manually run mmseqs searches of the contigs against the secondary databases.