Tools to remove duplicate or substring reads
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8.0 years ago
chjiao3456 ▴ 40

Is there any efficient tool to remove substring reads or duplicate reads from NGS data set? I know that readjoiner could remove the duplicated reads, but seems not work on substring reads. Thanks.

Example: Duplicates: read1: AGTCAT read2: AGTCAT In this case, only one read will be kept.

Substring: read1: GTCA read2: AGTCAT In this case, read1 will be removed.

next-gen sequencing alignment • 1.6k views
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8.0 years ago

The most efficient tool for this purpose is Dedupe from the BBMap package. However, it requires all reads to be stored in memory, so it needs a lot of memory. Can you explain in more detail what you are trying to do?

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Thanks for your help. I have added examples in the question.

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8.0 years ago
chjiao3456 ▴ 40

Just noticed that SGA tool is able to do this. Collapse Reads That Are Substrings Of Other Reads In Same Library

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