What tool can compute SNPs from a set of assemblies and output the SNPs into a dataframe?
I have several assemblies all from the same bacterial strain. I want to do a SNPs analysis but I'm having trouble finding tools that will do this and output the data into a dataframe of SNPs by position.
I have the fasta files for each assembly along with the shotgun genomic reads that went into (some of) them.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to download multiple fasta sequences and keep them organized by what genome they came from
written by ATS •
-
do we clone sequences while performing shotgun sequencing on microbiome?
written by fyfes •
-
Can any long read assemblers incorporate both nanopore and pacbio reads in the same run?
written by O.rka
-
How to download genome assemblies from NCBI with a list of GCA identifiers?
written by O.rka
-
What are the recommended methods for merging de-novo assemblies?
written by O.rka
-
Separate the Longest Strain in Bacteria
written by Shelle •
-
How can I pick up reads belongs to one isolates from shotgun metagenome
written by xuling2015 •
-
Change NCBI fasta file headers to makeblastdb format
written by chland •
-
How to identify the haplotypes in the Venter diploid genome
written by olga.botvinnik •
-
Set Up Soapdenovo (Or Just A Fasta File Of Scaffolds) For Ncbi Wgs Genome Submission
written by John St. John
