Definition of long and short read in wochenende

[arpit20328]

Hi

Wanted to know till what base pair, do wochenende will take input as short read and long read.

I have region of interest spanning 1500-1600 base pair... should I enter --aligner minimap2long or --aligner minimap2short

[colindaven]

Hi Arpit.

I'm not sure what you're trying to do here - to map a single region of interest to a metagenome reference ?

If so, that is really not what the tool was created for. It ist expecting reads as input, either short or long, but not regions. Perhaps it will map the region, but it is likely to get filtered out later - you might need to look in the initial BAM file to check for alignments. This is completely untested.

But definitely --aligner minimap2long .

Or did I misunderstand your intention, and you want to map long reads to a target ?

Generally, I think bwa mem is good/best for short reads 70 -300 ? bp, and minimap2short is for maybe 100-500bp
and minimap2long for 3-5kbp and longer sequences (using minimap2's map-ont setting).

In general you can see this in the code following the -x and check more in detail in the minimap2 manual and repo.

    if "minimap2long" in aligner:
        alignerCmd = [
            path_minimap2,
            "-x",
            "map-ont",
            "-a",
            "--split-prefix",
            prefix,
            "-t",
            str(noThreads),
            str(index),
            stage_infile,
            ">",
            minimap_samfile,
        ]
    elif "minimap2short" in aligner:
        alignerCmd = [
            path_minimap2,
            "-x",
            "sr",
            "-a",
            "--split-prefix",
            prefix,
            "-t",
            str(noThreads),
            str(index),
            stage_infile,
            ">",
            minimap_samfile,
        ]