Hello, Recently I came to quite a few Ion Torrent data (from SRA). For my project I would need to map them on few of my sequences. From what I read the best option is TMAP? But I have problems compiling it (which seems to be common problem with this software). Is there any other program that could handle this? I read something about Bowtie2? Best would be something I can use on Linux and put somewhere in my script (it's a lot of samples to do manually e.g., Geneious). I'm used to Illumina data and I'm struggling a bit so I will be grateful for any help.
Just bwa-mem or bowtie2, no magic here. Here is a comment from the bwa developer saying exactly that ion torrent alignment software
I just read the bwa manual. It says that bwa-mem supports Ion Torrent data. That could have save time to all of us :). Thank you!!
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You could try a conda install here, if you'd still like to use tmap. I'd recommend ATpoint's answer though.