There is a request to break fasta file by nucleotide (N) i.e if a sequence contains "N" or multiple "N"s,  break the sequence into parts before and after Ns. Headers must continue the names with consecutive numbers.

Input fasta:
=======================
>chr1
ATCGCTGATCGATNCTAGCTAGCTAGCGTAGCTGCTAGNCGTAGCCGTAGCT
>chr2
CCTGANGTAGT
>chr3
ATGNNNNNN
>chr4
NNNNCnT
==========================
Output fasta:
==========================
>chr1
ATCGCTGATCGAT
>chr1_2
CTAGCTAGCTAGCGTAGCTGCTAG
>chr1_3
CGTAGCCGTAGCT
>chr2
CCTGA
>chr2_2
GTAGT
>chr3
ATG
>chr4
C
>chr4_2
T
===========================
using awk:
===========================
$  awk '{gsub("[Nn]+","\n>\n");}1' test.fa | awk '/^>/ {if ($0 == ">") {$0=prev} prev=$0}1' | awk '/^>/ {getline seq} {if(seq!="") {print $0"\n"seq}}' | awk '(/^>/ && a[$0]++) {$0=$0"_"a[$0]}1'
===========================