how to use a chromosome scale reference genome to place scaffold of a closely related species
We have recently sequenced a close wild relative of pigeonpea using PacBio and scaffold the contigs with optical mapping. Now I would like to place/assign those scaffold to the chromosome. Hence, I was wondering how to use the reference genome of pigeonpea which is a chromosome scale for placing scaffold of its wild relative to chromosomes. Please suggest any tool or strategy.
• 1,202 views
•
link
updated
by
Michael Dondrup
•
written
by
nagarsaggi •
•
written
by
nagarsaggi •
1 answer
Mauve should work for that. Has a GUI viewer for inspecting alignments too and handles more than two species if required.
The web-site says it is no longer maintained but as long as it works for you it should be fine. Can be installed with BioConda.
• 0 views
•
link
written
by
Michael Dondrup
Log in to answer this question.
More posts like this
-
how to extract centromeric regions from human assemblies/FASTA
written by Matteo Ungaro •
-
Use Hi-C Sequence Data of close relative for scaffolding of genome.
written by SomeOne •
-
haploid genome phasing using close relative
written by Amy •
-
How to deal with heterozygous genome assemblies for inversions, INDELs?
written by anikcropscience •
-
Heatmaps with R for GC content
written by Charles.G •
-
need to map scaffolds to chromosomes: have mashmap outfile
written by truebeliever24 •
-
how are alleles represented in the sequenced reads?
written by lait
-
Extraction of genomes from mixed metagenomic samples
written by zimmlerten •
-
How are the GRC alt locus to primary assembly alignments generated?
written by anovak
-
scaffolding denovo contigs to genome
written by iraun
