Hello Biostars !
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 specififed 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 !