Convert several contig file of whole genome sequence into a raw nucleotide sequence

Question

[microorganism_001]

I have an assembled genome of many contigs in a fasta file which I get from a sequencing company. I want to make this all set of contigs into a full genome sequence fasta file without contig, is it possible? Is there any tool or program? A contig is a contiguous sequence of a genome based on a reference but I want the raw nucleotide sequence of Genome. Thanks.

[Pierre Lindenbaum]

you asked many question: comment and/or validate them: issue regarding download SRA file in bulk ; Query regarding genome coverage in de-novo assembly ; error to run rnammer ; Installation error of hmmer ; How to remove binary files which are installed into /usr/local/bin

Answer 1

[akshay]

Your genome was assembled up to the contig level, possibly due to data limitations. If you wish to enhance contiguity, you can employ reference-based scaffolding using tools such as RagTag, especially if a reference genome is available.