Read trimming

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Read trimming is a pre-processing step in which input reads are trimmed at either end, removing bad data. The result of read trimming is the file reads.trim_lr, which indicates the locations on either end of each read at which to trim.

Types of read trimming include:

  • Quality trimming: In Sanger and Solexa reads, the trace signals tend to get weaker toward the end of the read, resulting in more mis-calls and lower quality scores. The ends of these reads are often worse than useless, aligning in places where they should not. Quality trimming removes these ends.
  • Vector trimming

Reads may be deliberately un-trimmed during the assembly process; for an example, see the module UntrimToCloseGap.

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