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## Contaminant removal ##
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:warning: Decontamination can be skipped in the config file by turning `decontamination` into `False`
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Contamination during sequencing experiment is unavoidable. Thus, it's necessary to remove sequences which are not supposed to be there. The common approach is to map reads against contaminant targets and to extract reads that does not mapped. For this task, we used [fastQscreen](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/_build/html/index.html) with --nohits flags to extract reads which are not mapped against references. FastQscreen have integrated references (Human, Mouse, Adapter, Arabidopsis, Drosophilia, Ecoli, Lambda, Mitochondria , PhiX, Rat, rRNA and vectors) but you can add your own targets within the config file. If personal references is preferred over fastQscreen references, you can avoid downloading them by setting dl_genomes (within config file) to False.
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