I am currently looking for a tool similar to fastq screen: https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_documentation.html, which is able to roughly characterize genome composition (Did we sequenced the right species? Do we have contamination in our sequences?) with nice graph directly from a subset sample of fastq reads (like showing the amount of hits for several species and such).
I will probably try fastq screen, but it is specified that the tool may be more suitable for short reads technologies as it use short read aligner such as bowtie2. I thought maybe such a tool exist for longer and more erroneous reads. Or maybe a combination of a suited aligner (like ngmlr for long reads and higher error rate awareness) and then an other tool could do it?
Does anyone have any ideas or suggestions? I'll keep you updated on my own findings!