ngs view

Overview

The ngs view utility prints various next-generation sequencing files formats to the stdout stream. This command also effectively acts as a linter, as any files that are not within spec (as defined by noodles) will throw an error.

The following file formats are supported or are scheduled to be supported in the near future.

File Format	Supported	(Predicted) Version Support Included
SAM	✅	Released in v0.4.0
BAM	✅	Released in v0.4.0
CRAM	✅	Released in v0.4.0
GFF	❌	Scheduled for 0.5.0 (issue)
GTF	❌	Scheduled for 0.5.0 (issue)

Mode

ngs view supports three different viewing modes:

• --mode full. Prints both the header and the records within the file.
• --mode header-only. Prints only the header (and not the records) of the file.
• --mode records-only. Prints only the records (and not the header) within the file.