This small python code re-builds the contig sequence from the 'a' lines of the miniasm output. It is designed to work around an unexplained issue where miniasm outputs contigs looking like 'NNNNNNNNN'.
usage: python build_seq_from_miniasm.py [-h] --assembly ASSEMBLY --reads READS
--output OUTPUT
build_seq_from_miniasm : to rebuild the contigs from the 'a' lines and the
fasta/q file
optional arguments:
-h, --help show this help message and exit
--assembly ASSEMBLY Assembly from miniasm, in GFA format with or without
the contig sequences
--reads READS Fasta/q file of the reads used to build the assembly
--output OUTPUT Output file in GFA format