Host removal parameter - pre-built bowtie2 index

[simone-pignotti]

Description of feature

Hi,

In the host removal module, the bowtie index needs to be recomputed from --host_fasta for each execution. Would it be possible to add --host_bt2 or similar to point to a pre-built index prefix? The logic is already implemented for the --host_genome option, where pre-built indexes from iGenomes are used.

Thanks Simone

[hkaspersen]

Hello! I second this, the host genomes I use are quite big, and by having this option it will significantly reduce runtime of the pipeline

[jfy133]

I agree, it's a good idea. This should be relatively straightforward to add, will schedule it for the next release :+1:

[Thomieh73]

@jfy133 hey, is this idea already implemented. I am trying to run it with a large host genome file, and I get the error that bowtie build needs the setting: --large-index. I already have a prebuild index for Bowtie, so if this option is available than I rather use that.

[jfy133]

Hi @Thomieh73

Sorry not yet, the request just came before I started parental leave and slipped through the cracks...

But I'm almost at the end of my leave and ramping up work again, so barring any other interruptions I can try and do this soon

[Thomieh73]

Okay, I can understand that. I am trying figure out a work around in the meantime. With the Taxprofiler pipeline, I used my bowtie host genome index, and I cleaned the files then. I could use those cleaned files with this pipeline.

[jfy133]

yes, that's a good idea :)