Question: Mapping contigs to a reference genome
1
gravatar for SpamChop
9 days ago by
SpamChop10
Edinburgh, UK
SpamChop10 wrote:

Hi!

I have ~163000 contigs (a single FASTA file) and I want to map them to a refernce genome (also a FASTA file). Is there any way to do it? I have tried bowtie2, but could not work out its nuances.

Any help appreciated!

Thanks

alignment genome • 140 views
ADD COMMENTlink modified 9 days ago by evelyn30 • written 9 days ago by SpamChop10
2

Is this a related reference (i.e. you expect high homology)? If so you could use blat or even blast+. If these are very large contigs a program like LASTZ would also be valuable.

ADD REPLYlink written 9 days ago by genomax68k
1

Try minimap2 with preset -x:

asm5/asm10/asm20: asm-to-ref mapping, for ~0.1/1/5% sequence divergence

ADD REPLYlink modified 9 days ago • written 9 days ago by SMK1.3k
2
gravatar for h.mon
9 days ago by
h.mon25k
Brazil
h.mon25k wrote:

Bowtie2 is a short read mapper and, although it can be used to map long sequences, it probably won't be good at it, specially if the query and reference are even moderately divergent.

In addition to the suggestions by SMK and genomax , there is also LAST.

Another option to consider is QUAST, an assembly evaluation tool. Quast uses minimap2 to align one (or more) query genomes to a reference genome, and in addition to the alignment, it will provide a number of metrics comparing the query to the reference.

ADD COMMENTlink written 9 days ago by h.mon25k
1
gravatar for Corentin
9 days ago by
Corentin290
Corentin290 wrote:

Hi,

You can use D-genies, it can map two fasta to produce a dotplot (http://dgenies.toulouse.inra.fr/)

Alternatives are:

If you are more interested in ordering your contigs, then you could try "show-tiling" from Mummer

ADD COMMENTlink written 9 days ago by Corentin290
0
gravatar for evelyn
9 days ago by
evelyn30
evelyn30 wrote:

You can try nucmer from mummer:

nucmer -p output_prefix ref.fa example-contigs.fa
ADD COMMENTlink written 9 days ago by evelyn30
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