The best tool for Scaffolding
Hello, I would like to know if somebody can you advice me to choose the best scaffolding tool (for bacterial genome)?
I get contigs from Spades, and would like use the assembly with nextstrain for snp analysis
Thank you
• 1,015 views
•
link
updated
by
dthorbur
•
written
by
davidmaimoun •
•
written
by
davidmaimoun •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Contigs Input For Phylogenetic Tree
written by davidmaimoun •
-
Contigs number vs NNN gap % in WGS
written by Pegasus •
-
Tools for reference-guided de novo assembly of bacterial genome
written by Bushra Bibi
-
How/why contigs and scaffolds end up being identical in number and length by spades de novo assembl…
written by dejenieshif •
-
Bacterial genome hybrid assembly
written by A_heath •
-
Scaffolding of bacterial genome assemblies
written by Jelo •
-
contigs of spades
written by sami •
-
(Scaffolding ) Gap Closer - Gap Filler , SSPACE
written by Bioinfo •
-
Assembly contigs into scaffolds with AMOS
written by ben.blais •
-
I need to get the fold-coverage
written by kamel •
Can you provide more information on what data you have? Chances are without something like optical mapping, high quality long read data, and/or Hi-C, you're only going to get a contig level assembly.
Also, there is nothing stopping you from SNP calling with a contig level genome, but if made up of lots of small contigs you will lose a reasonable amount of data.