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Old 06-07-2017, 02:33 AM   #1
cr517
Junior Member
 
Location: UK

Join Date: Jun 2017
Posts: 1
Default Can't find show-aligns in mummer

Hi,

I am trying to use mummer: http://mummer.sourceforge.net/manual/#mappingdraft

to align a contig to a reference genome using:

nucmer --prefix=ref_qry ref.fasta qry.fasta

show-coords -rcl ref_qry.delta > ref_qry.coords

show-aligns ref_qry.delta refname qryname > ref_qry.aligns

show-tiling ref_qry.delta > ref_qry.tiling

I have managed to do the first two commands but at the third, it tells me that 'show-aligns' is not found. 'show-tiling' is found though. I have installed mummer through brew with brew install homebrew/science/mummer. Does anybody know how I can get the show-aligns function?

==> Installing mummer from homebrew/science
==> Downloading https://homebrew.bintray.com/bottles...er-3.23.sierra.
Already downloaded: /Users/cr517/Library/Caches/Homebrew/mummer-3.23.sierra.bottle.3.tar.gz
==> Pouring mummer-3.23.sierra.bottle.3.tar.gz
🍺 /usr/local/Cellar/mummer/3.23: 143 files, 6.5MB

~ which mummer
/usr/local/bin/mummer

3.23 pwd
/usr/local/Cellar/mummer/3.23
➜ 3.23 ls
ACKNOWLEDGEMENTS combineMUMs nucmer2xfig
COPYRIGHT delta-filter promer
ChangeLog dnadiff repeat-match
INSTALL docs run-mummer1
INSTALL_RECEIPT.json exact-tandems run-mummer3
LICENSE gaps scripts
Makefile mapview show-aligns
README mgaps show-coords
annotate mummer show-diff
aux_bin mummerplot show-snps
bin nucmer show-tiling


Thanks a lot.

C.
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