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What Is 'Read Length' In The Context Of Simlibrary?

What does read length mean in the context of the SimLibrary software? The program has an option '-r' which is said to mean 'Read length to sample. Affects the total length of fragments produced and the total number of fragments produced via the coverage '. The webpage is here: http://www.ebi.ac.uk/goldman-srv/simNGS/simNGS/man/simLibrary.1.html

From what I understand, SimLibrary simulates the generation of fragments from the genome.

So, I'm confused by the term 'read length' which makes me think of the term 'read length' or 'tag length' which would be relevant to the simulation of the actual sequencing with simNGS for instance.

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updated by Biostar Biostar • written by KCC KCC

1 answer

In simLibrary terminology the fragment size (the total length of the generated fragment) in single-ended mode is equal to the insert size (<tt>-i</tt>) plus the read length (<tt>-r</tt>). However in paired-end mode the total fragment size equals the insert size plus twice the read length. This behaviour is the reason for specifying the read length, despite the fact that simLibrary does not deal with the simulation of the reads itself.

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written by Botond Sipos Botond Sipos

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