Removal of unwanted character "N" from Assambly and Annotated file of whole genome sequemce

Question

[tasmina.fm]

We are working with assembly and annotation of whole genome sequence of bacteria with Linux command (soapdenovo2 and some related software). After assembly and annotation, we got unwanted character N within the fasta file. For this reason, we are not able to analyze it. Would you please help us how can remove it from whole genome sequence fasta file??

[ATpoint]

For this reason, we are not able to analyze it => Why not?

N means ambiguous characters that might arise due to repetitive / difficult-to-sequence regions. Most genome assemblies contain them to some extend. The human reference (GRCh38) has > 150mio of them. Is this a short-read assembly?

[GenoMax]

we got unwanted character N within the fasta file

While you may not want the N they likely signifies that your bacterial genome assembly is not complete. It is not unusual to see this especially if you are only using short-read data. You may need to investigate and re-do the assembly (repeat regions and over-sequencing can cause issues) or add long-read coverage (e.g. PacBio/Nanopore) to truly complete the assembly.