Are there any tools that can report all areas of very low coverage or areas of high coverage in NGS data?
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I've written some custom code to programatically do this, but it only works on a few assembly formats (don't have time or funding to add more formats yet). But several assembler programs have ways to output the coverage levels of the contigs. It would then be up to you to parse that output and find any locations that are below or above your thresholds.
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Originally posted by willMD View PostAre there any tools that can report all areas of very low coverage or areas of high coverage in NGS data?
If you do have a bam file of aligned reads to a reference sequence then you will be able to generate a plot of the per-base coverage of the reference sequence using bedtools genomeCoveragebed.
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