Checkpoint 2: Read extraction

Section: Data [5/5].

• what is extraction and why do we need to do that?
• why can't we simply use multi-purpose base quality programs (e.g. FastQC) for long-reads quality check?
• in ONT, how many "template" reads do we need to constitute a 2D read? and a 1D² read?
• what are the most common formats of data delivery from PacBio?
• are all "extractor" software the same? if not, what are the differences and functionalities? (hint: -h)
• how can you assess the "raw" reads quality?

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