<p>Depending on how long the reference sequence is, you may have success using <a href="http://emboss.open-bio.org/rel/rel6/apps/diffseq.html" rel="nofollow noreferrer">diffseq</a> from the EMBOSS tools package.</p>
<p><a href="http://emboss.open-bio.org/" rel="nofollow noreferrer">http://emboss.open-bio.org/</a></p>
<p>I've used diffseq for comparing assembled plasmid and mitochondrial sequences to a reference genome.</p>

CC BY-SA 4.0
2024-06-29T03:00:11.950Z
2024-06-29T03:00:11.950Z
gringer
<p>If you want a ready-to-use solution, I can suggest <a href="https://sanger-pathogens.github.io/snp-sites/" rel="nofollow noreferrer">SNP sites</a>. I used it in the past, and it worked perfectly. This paper might help further <a href="https://https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320690/" rel="nofollow noreferrer">Link to paper</a>.</p>
<p>Make sure that your sequences are aligned before you start. MAFFT can address that issue.</p>

CC BY-SA 4.0
2024-07-01T18:37:05.497Z
2024-07-01T18:37:05.497Z
ozankiratli
<p>I have experience in obtaining a variant calling file from NGS sequencing files using the Samtool/bedtools workflow. However, when we receive pre-assembled sequences, it becomes challenging to apply this workflow due to the structure of the assembled fasta file. Is there a method, program, or workflow that allows me to identify SNPs from an assembled fasta file?</p>
<p>Thank you very much.</p>

CC BY-SA 4.0
2024-06-28T08:54:03.680Z
So you are working with a species that has a sequenced and annotated reference genome and then you sequence specific individuals of that species and get back an assembled genome? What is the species? What kind of assembly? Do you get full chromosomes? Contigs? Are you looking for coding variants? All variants? Do you have a list of known gene sequences? Please edit your question and give us some context to understand your data.
terdon
<snp><samtools><mutations>
How to Call SNPs from Assembled Fasta Files?
# How to Call SNPs from Assembled Fasta Files?

(Asked by: username_0 on 2024-06-27)

I have experience in obtaining a variant calling file from NGS sequencing files using the Samtool/bedtools workflow. However, when we receive pre-assembled sequences, it becomes challenging to apply this workflow due to the structure of the assembled fasta file. Is there a method, program, or workflow that allows me to identify SNPs from an assembled fasta file?

Thank you very much.

**Tags:** snp, samtools, mutations
> **Comments:**
> **username_1**: So you are working with a species that has a sequenced and annotated reference genome and then you sequence specific individuals of that species and get back an assembled genome? What is the species? What kind of assembly? Do you get full chromosomes? Contigs? Are you looking for coding variants? All variants? Do you have a list of known gene sequences? Please edit your question and give us some context to understand your data.  

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## 2 answers

### Answer by username_2 on 2024-06-29. Score: 1

Depending on how long the reference sequence is, you may have success using [diffseq](http://emboss.open-bio.org/rel/rel6/apps/diffseq.html) from the EMBOSS tools package.

<http://emboss.open-bio.org/>

I've used diffseq for comparing assembled plasmid and mitochondrial sequences to a reference genome.


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### Answer by username_3 on 2024-07-01. Score: 1

If you want a ready-to-use solution, I can suggest [SNP sites](https://sanger-pathogens.github.io/snp-sites/). I used it in the past, and it worked perfectly. This paper might help further [Link to paper](https://https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320690/).

Make sure that your sequences are aligned before you start. MAFFT can address that issue.


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