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You may not want to use the entire workflow of MOSCA. Here follow some interesting examples of tasks that are better executed running parts of MOSCA separately. The following commands assume you have installed MOSCA [as instructed](https://github.com/iquasere/MOSCA/wiki/Installing-MOSCA).
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## Preprocess NGS reads
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MOSCA's preprocessing script can be used standalone, as it automatically downloads all resources required.
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```
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python ~/anaconda3/envs/mosca/share/MOSCA/scripts/preprocess.py -i {your input reads (e.g. mg_R1.fq,mg_R2.fq)} -t {number of threads} -o {output directory} -adaptdir {resources directory}/adapters -rrnadbs {resources directory}/rRNA_databases -d {data_type (either "dna" or "mrna")} -rd {resources directory} -n --minlen {minimum length of reads to keep} --avgqual {minimum average quality of reads to keep}
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``` |
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