Bioinformatics with Python Cookbook - Second Edition

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Sometimes, reference genomes carry extra information, for example, the Anopheles gambiae genome is soft masked. This means that some procedures were run on the genome to identify areas of low complexity (which are normally more problematic to analyze). This will be annotated by capitalization: ACTG will be high complexity, whereas actg will be low.

Reference genomes with lots of scaffolds are more than an inconvenient hassle. For example, very small scaffolds (say, below 2,000 bp) may have mapping problems when using an aligner (such as Burrows-Wheeler Aligner (bwa)), especially at the extremes (most scaffolds will have mapping problems at their extremes, but these will be of a much larger proportion of the scaffold if it's ...