How to use spades and set minimum coverage

[Stupid747]

Thanks for a great program. I’m new at linux and ariba so this might be stupid question. I wonder what is the command for setting spades as the assembler when performing a run.

I thought it was “ariba run [--assembler spades] ref reads_1.fq reads_2.fq output_dir

but I get error argument.

I also wonder if its possible to set a minimum coverage? We experience carryover between some sample when doing multiplexing in Illumina and we get a hit on genes we know are wrong, with few reads (around 5-10) and ctg_cov around 1-2.

Thanks for the help

[martinghunt]

Re spades: that command looks correct. What error do you get? But in any case, unless you have a compelling reason for using spades, I recommend using the default assembler instead.

Re min coverage: you can filter the output file on the ctg_cov column, which is the mean read depth across the contig.

[Stupid747]

when running the command I get

"ariba: error: unrecognized arguments: reads_2.fq output_dir

[martinghunt]

What was the exact command that you ran?

[kpepper]

This issue would have been caused by a mismatch/error in the program arguments provided. Closing due to age.