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There are various software for simulating reads for Next Generation Sequencing. Can anyone tell what exactly is done by a read simulator software

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  • $\begingroup$ Welcome at Biology SE! Your question is interesting althoughI fear it is more related to informatics than biology. The actual algorithms and the internal workings of a software is off topic here. $\endgroup$ – Nandor Poka May 4 '15 at 9:28
  • $\begingroup$ I'm voting to close this question as off-topic because algorithms and internal software mechanism are not related to biology. $\endgroup$ – Nandor Poka May 4 '15 at 9:29
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    $\begingroup$ @poka.nandor it is not in a true sense about a general algorithm; it is a algorithm that simulates a biological experiment and so it should be on-topic. Likewise, mathematical models for biological experiments are also on-topic and we do have many questions on that subject. However, I think that the OP could have put in some more effort. $\endgroup$ – WYSIWYG May 4 '15 at 11:01
  • $\begingroup$ @WYSIWYG perhaps you're right, I agree with you that bioinformatics and mathematical biology should be on topic. I think it depends on how deep the OP is interested in the software. As a programmer I may have jumped to the point to assume that the OP is interested in exact algorithm implementation instead of general features. In the first case I think it's off topic, the latter case could pass as on topic. Until further clarification I'll uphold my close vote, but as always I'm willing to retract.... $\endgroup$ – Nandor Poka May 4 '15 at 11:43
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In general, a read simulator does the following:

  1. Selects regions from a reference sequence with some sort of predefined or user-specified size distribution.
  2. Converts the sequence from those regions into single or paired end reads with quality scores. The quality scores and read lengths are typically user defined.
  3. Introduces errors into the aforementioned sequences, typically with more at the 3' end, which matches what comes from a sequencer.

A simulator may also try to reproduce the uneven coverage that you'd see in real data. In any case, most simulators will place the original coordinates of the simulated reads in the read names so that the quality of the resulting alignments of the reads can be assessed.

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