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By default the NCBI GX tool hard masks internal contaminants. Hard masking already has multiple meaning. First, it can represent a gap. Second, it can represent hard masking by a tool such as repeat masker. Now with this, it can also mean hard masking due to contamination.
Some suggestions:
Adaptors should be removed by the assembler software.
Foreign organism contamination should be removed following the recommendations from NCBI FCS GX (https://github.com/ncbi/fcs/wiki/FCS-GX-output#fcs-gx-action-report), except for the FIX action for internal contaminations. Instead of hard masking the contamination, we should insert 100 N's there to denote a gap of unknown size.
GallVp
changed the title
Auto remove the contamination
Auto remove the contamination?
May 6, 2024
No description provided.
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