ShoRAH: Illumina reads ; influenza

[LauraVP1994]

Dear,

I am very interest in using your tool for my project. I'm working on influenza reads that were sequenced with Illumina MiSeq. I was able to extract quasispecies with LoFreq, however LoFreq doesn't have the ability to construct haplotypes, therefore I turned to this tool. However, I tried running this, but I encounter always an error:

/usr/local/bin/b2w: error while loading shared libraries: libhts.so.2: cannot open shared object file: No such file or directory

I also tried this with the amplicon example that was given, but same error was given. I don't know if you have an idea what could be the cause of this?

Additionally, I also was wondering what parameters would be ideal as I don't find a lot of information. Based on a few papers I think that for my purpose following command should work: shorah shotgun -b sample_sort.bam -f sample.fasta -a 0.01 -w 120 -s 3

However, I don't know if the other parameters should be set or if the default is sufficient?

Kind regards and thanks in advance Laura