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Genomics resources for the long-term evolution experiment with Escherichia coli.
For related information and data, see also:
If you would like to browse mutations in specific strains or genes on the web, there is an interactive interface to the LTEE genomics data here: http://barricklab.org/shiny/LTEE-Ecoli/
To get started with using these data files for an analysis, download a release version of the repository.
Lists of mutations in clonal isolates from the long-term evolution experiment in GenomeDiff format. This format is described in the breseq documentation.
Lists of mutations in clonal isolates from the mutation accumulation evolution experiment in GenomeDiff format. This format is described in the breseq documentation.
Output of mutation counts, phylogenetic trees, etc. generated from the curated GenomeDiff files. Counts in these files reflect removing mutations in repetitive regions (masked files) and/or mutational hotspots adjacent to IS elements (no_IS_adjacent files).
Scripts used for performing curation and generating summary output files.
Important: Install a version of breseq that is compatible with the version of the LTEE-Ecoli files that you are using (as specified for the release that you downloaded) AND run these commands from the main LTEE-Ecoli path.
This command generates files giving counts of different mutations, phylogenetic trees for each population, HTML tables showing mutations in each population, etc. These all appear in the summary directory.
bash bin/summary.shmkdir -p fasta
gdtools APPLY -f FASTA -r reference/REL606.gbk -o fasta/Ara-1_20000gen_8593A.fna LTEE-clone-curated/Ara-1_20000gen_8593A.gdmkdir -p fasta
cd LTEE-clone-curated; ../bin/batch_run.pl -0 "gdtools APPLY -f FASTA -r ../reference/REL606.gbk -o ../fasta/#e.fna #d"