hostile

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Selection of appropriate reference genomes (indexes)

4

Hi, the software seems very good, but I am new in metagenome analysis and I have questions about the selection of appropriate reference genomes (indexes) when using 'hostile'. 1. I...

DrYoungOG

Currently this is hardcoded. It would be nice if this could be overridden using an environment variable

bede

Support accepting stdin instead of a specific filepath for single ended data

2

A common use I have for hostile is to cleanup and concatenate a directory of fastqs prior to moving them off instrument, if I could do all of this with...

BioWilko

Thanks for providing us with hassle-free and fast dehosting tool. I am however running into an issue when using PE fastq files and providing the custom reference fasta file of...

Rohit-Satyam

For whatever reason, when initially implementing long read support using Minimap2, I was unable to demonstrate significantly reduced execution time versus recreating the index from scratch every time `hostile clean`...

bede

Hostile with no options classifying different than --invert

3

Hi and first, thanks for the great work. I tried to run Hostile to get the filtered result files and the removed read-pairs (Illumina paired-end data as input). What caught...

jannikseidelQBiC

Evaluate Minimap2 2.28 and Bowtie2 2.5.4 for pinning

bede

Allow adding of Illumina Casava 1.8 format entry to fastq headers

2

Hi, Thanks for the useful tool. Would it be possible to add the option to modify the headers of the output fastq files? I can see in `aligner.py` that the...

charlesfoster

Metatranscriptome performance

9

Hey @bede, Thanks for great tool! I've included it in my pipeline for host-microbiome dual transcriptomics, and our lab has been using it on a variety of projects. I've been...

sterrettJD

Nicely handle corrupt Minimap2 indexes, build at fetch time?

2

Since 2.0.0, MMI files are created on the fly if they do not already exist when `hostile clean` is invoked. In subsequent runs the `.mmi` version of the index is...

bede