Mapping a small number of contigs to a reference subsequence

Mapping a small number of contigs to a reference subsequence

1

Hello,

Is there a method or a tool to align/map a small number of contigs (obtained with Canu) to a subsequence extracted from a reference genome ?
For example,in a similar way to reads to reference assembly (using bwa mem, bowtie, minimap, etc), I want to align/assemble 6 contigs that span a region of interest to the reference sequence and to visualize the mapping (using Tablet, IGV, UGENE, etc.) with the overlap regions and gaps.

Or, is it possible to assemble “de novo” only a small number of contigs (that cover a specific region) into a bigger scaffold and align the sequence obtained to a reference subsequence ?

Thank you !


align


genome


mapping


assembly


contigs

• 37 views

disclaimer: I’m a JBrowse 2 developer

I think @GenoMax ‘s advice is good, you can align the contigs vs the reference as is. Then, you could use JBrowse 2 (jbrowse.org/jb2) to visualize those alignments. Minimap2 for example will output a PAF file, and JBrowse 2 can visualize PAF files in a “synteny style” view

Here is a basic set of command line steps you can use for setting this up

npm install -g @jbrowse/cli
jbrowse create newdir # folder containing jbrowse 2 html,js,css etc

# samtools faidx creates fasta index
samtools faidx ref.fa
samtools faidx contigs.fa 

# add-assembly will copy your ref fast to the newdir
jbrowse add-assembly ref.fa --out newdir --load copy
jbrowse add-assembly contigs.fa --out newdir --load copy

# run alignment, the -c adds CIGAR strings creating base level alignment
minimap2 -c ref.fa contigs.fa > comparison.paf

# add the paf file as a "synteny track" in jbrowse, the assemblyNames is flipped in order that the minimap2 command uses
jbrowse add-track comparison.paf --assemblyNames contigs,ref --out newdir --load copy

# load gene annotations perhaps for the reference genome
jbrowse add-track ref.gff --out newdir --load copy --assembly ref
# may not have them but can load annotations predicted on the contigs also
jbrowse add-track contigs.gff --out newdir --load copy --assembly contigs

# start a simple http server in the newdir folder
cd newdir
npx serve
# open up http://localhost:3000 in your web browser

If you don’t want a web server, you can also use “JBrowse Desktop” which is just a installer you can run (jbrowse.org/jb2/download/) but the CLI with the web server is easier to illustrate in a short number of steps

Then you can get dotplots or ‘synteny style’ views like this jbrowse.org/jb2/docs/user_guides/linear_synteny_view/


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