https://github.com/ctb/2014-megahit-evaluation

https://github.com/ctb/2014-megahit-evaluation

Last synced: 5 months ago
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• Host: GitHub
• URL: https://github.com/ctb/2014-megahit-evaluation
• Owner: ctb
• License: other
• Created: 2014-10-09T00:22:45.000Z (over 11 years ago)
• Default Branch: master
• Last Pushed: 2014-10-11T03:38:51.000Z (over 11 years ago)
• Last Synced: 2025-01-30T23:48:30.890Z (over 1 year ago)
• Size: 141 KB
• Stars: 6
• Watchers: 2
• Forks: 2
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

          
Grab the data here:

     curl -O https://s3.amazonaws.com/public.ged.msu.edu/ecoli_ref-5m.fastq.gz

Subset it like so:

     gunzip -c ecoli_ref-5m.fastq.gz | head -4000000 | gzip -9c > ecoli_ref-1m.fastq.gz

     gunzip -c ecoli_ref-5m.fastq.gz | head -2000000 | gzip -9c > ecoli_ref-500k.fastq.gz

Grab the E. coli genome:

     curl -O https://s3.amazonaws.com/public.ged.msu.edu/ecoliMG1655.fa.gz

     gunzip ecoliMG1655.fa.gz

Install QUAST (http://bioinf.spbau.ru/quast) somewhere, edit Makefile appropriately.

Build MEGAHIT (https://github.com/voutcn/megahit/) somewhere, edit Makefile appropriately.

Install SPAdes (http://bioinf.spbau.ru/spades) somewhere, edit Makefile appropriately.

Run 'make all'.

----

The Makefile is under the BSD license; please see the LICENSE file.