Convert SRA to FastA I'm trying to get the FastA files for some accessions (like NC_001416.1). I did not managed to find an FTP server or direct link to these files (I want to get it from command line with wget, not from a web browser). But I found an "equivalent" file in ftp://ftp.ncbi.nlm.nih.gov/sra/refseq/NC_001416.1

This file is an SRA file that should be processed with the SRA-toolkit. In particular, fastq-dump seems to be the tools of choice.

I ran

fastq-dump --fasta NC_001416.1


and I got a NC_001416.1.fasta file. But the file contains the sequence I'm looking for in chunks of 5000 bases. The IDs in the output file are:

&gt;NC_001416.1.1 length=5000
&gt;NC_001416.1.2 length=5000
&gt;NC_001416.1.3 length=5000
&gt;NC_001416.1.4 length=5000
&gt;NC_001416.1.5 length=5000
&gt;NC_001416.1.6 length=5000
&gt;NC_001416.1.7 length=5000
&gt;NC_001416.1.8 length=5000
&gt;NC_001416.1.9 length=5000
&gt;NC_001416.1.10 length=3502


I need that sequence under a single ID:

&gt;NC_001416.1 length=48502


I cannot find the proper parameters to supply to fastq-dump to achieve the desired result.

Does anyone know how could I get the FastA file I'm expecting? How to process properly the SRA file or where I could download the FastA file directly.
Finally, I found an alternative to the SRA translation: a link that works! For those of you interested in knowing how to download FastA files from NCBI using an accession number, try the following link:

https://www.ncbi.nlm.nih.gov/search/api/sequence/${accession}/?report=fasta


Using wget to download the accession used as example:

wget -O NC_001416.1.fasta "https://www.ncbi.nlm.nih.gov/search/api/sequence/NC_001416.1/?report=fasta"