minimap2 map-hifi support?

[kevinmyers]

I am attempting to map our PacBio data using coverm and the -x map-pb option:

coverm genome --interleaved ../pacbio_mapping/fastq_all/pacBio.ccs.fastq.gz -d ../fasta_files/individual_fasta_files/ -p minimap2-pb -x fasta

but I keep getting this output (with or without the --interleaved option):

[2022-06-28T14:44:58Z INFO  coverm] CoverM version 0.6.1
[2022-06-28T14:44:58Z INFO  coverm] Using min-covered-fraction 10%
[2022-06-28T14:44:58Z INFO  bird_tool_utils::external_command_checker] Found minimap2 version 2.24-r1122 
[2022-06-28T14:44:58Z INFO  bird_tool_utils::external_command_checker] Found samtools version 1.15.1 
[2022-06-28T14:44:58Z INFO  coverm] Profiling 217 genomes
[2022-06-28T14:44:58Z INFO  coverm] Generating concatenated reference FASTA file of 217 genomes ..
[2022-06-28T14:45:00Z ERROR coverm::mapping_parameters] Paired-end read input specified to be mapped with minimap2-ont or minimap2-pb, which is presumably incorrect. Mapping paired reads can be run via minimap2-no-params if -ont or -pb mapping is desired.

Looking at the minimap2 manual I see the following about PacBio reads and the -x option:

map-hifi | Align PacBio high-fidelity (HiFi) reads to a reference genome (-k19 -w19 -U50,500 -g10k -A1 -B4 -O6,26 -E2,1 -s200).
-- | --

map-pb | Align older PacBio continuous long (CLR) reads to a reference genome (-Hk19).
-- | --

Our PacBio are HiFi reads and so it seems likely that's why the command is throwing an error. Is the map-hifi option available in coverm? If not, am I able to set the parameters individually as indicated in the Minimap2 manual? Or is my command off for mapping PacBio samples?

[wwood]

Hi,

Interleaved is for paired-end files where both reads of each pair are in the same file. I think --single is probably what you are after for these?

Thanks for the tip re minimap2 map-hifi. I've added this option in the main branch, so this will be available in the next release after 0.6.1.
ben

[kevinmyers]

Thanks. I am running it with the --single option now.