Question: regenerating -contigs file in ABySS
0
gravatar for cmstouthamer
2.6 years ago by
United States
cmstouthamer0 wrote:

I accidentally deleted my -contigs file generated by an ABySS assembly, but I still have all of the other intermediate files.  How can I remake the -contigs file?

abyss assembly • 851 views
ADD COMMENTlink modified 2.6 years ago by benv620 • written 2.6 years ago by cmstouthamer0
3
gravatar for benv
2.6 years ago by
benv620
Canada
benv620 wrote:

If you rerun your abyss-pe command with the full name of the deleted contigs file as the last argument, it will do whatever is necessary to rebuild the file, i.e.

$ abyss-pe <... your abyss-pe params for assembly ...> myassembly-contigs.fa

or

$ abyss-pe <... your abyss-pe params for assembly ...> contigs

Replace "myassembly" in the first command with whatever the prefix is for your assembly files.

That's the beauty of 'make'. It will only run the commands that are necessary to build the target you specify.  Btw, it is always wise to run abyss-pe with the --dry-run option first, to see what it *would* do before actually running it, i.e.

$ abyss-pe <... your abyss-pe params for assembly ...> myassembly-contigs.fa --dry-run

Btw, myassembly-contigs.fa is just a symlink to myassembly-6.fa. So if you still have myassembly-6.fa, you can recreate myassembly-contigs.fa with:

$ ln -s myassembly-6.fa myassembly-contigs.fa

ADD COMMENTlink written 2.6 years ago by benv620

Thank you so much benv!  This worked perfectly!

ADD REPLYlink written 2.6 years ago by cmstouthamer0
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