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Bacterial contamination in human DNA sample

Hello

I need some suggestions. We have been facing problems with sequencing old DNA samples. Poor read length and yield. We suspect bacterial contamination in these human DNA samples and plan to analyze the contamination by performing the sequence alignment. Has anyone ruled out/ detected the contamination by any other methods

Thanks

Priya

long-read-sequencing bacterial-contamination
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updated by Ram Ram • written by priya.bmg • priya.bmg
  1. get 16s RNA sequences for prokaryotes
  2. Index them
  3. Edit the fastqscreen configuration file to include 16sRNA indices
  4. Use fastqscreen

You can also use microbiome tools such as sortmeRNA to detect 16sRNA sequences.

• 0 views • link
written by cpad0112 cpad0112

Try taxonomical classification of the reads using Kraken2 or similar tools.

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written by Arup Ghosh Arup Ghosh

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