AGAPE

AGAPE (Automated Genome Analysis PipelinE) for yeast pan-genome analysis is designed to automate the process of pan-genome analysis and encompasses assembly, annotation, and variation-calling steps. It also includes programs for integrative analysis of novel genes.

-- INSTALLATION --

Read "INSTALL.txt" file in the package

-- USAGE --

Read "README.txt" file in the package

Reference

Song G, Dickins B, Demeter J, Engel S, Gallagher J, Choe K, Dunn B, Snyder M, Cherry J (2015) AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae. PLoS ONE, 10(3): e0120671.

Name		Name	Last commit message	Last commit date
Latest commit History 33 Commits
bin		bin
cfg_files		cfg_files
reference		reference
src		src
ChainNet.sh		ChainNet.sh
INSTALL.txt		INSTALL.txt
README.md		README.md
README.txt		README.txt
adjust_annot.sh		adjust_annot.sh
agape_annot.sh		agape_annot.sh
agape_assembly.sh		agape_assembly.sh
agape_novel_genes.sh		agape_novel_genes.sh
assemble.sh		assemble.sh
combined_annot.sh		combined_annot.sh
configs.cf		configs.cf
error_correction.sh		error_correction.sh
final_annot.sh		final_annot.sh
homology_annot.sh		homology_annot.sh
hugeseq.sh		hugeseq.sh
infer-scaf-annot.sh		infer-scaf-annot.sh
intervals.sh		intervals.sh
maker.sh		maker.sh
non_ref.sh		non_ref.sh
non_ref_contigs.sh		non_ref_contigs.sh
novel_orfs.sh		novel_orfs.sh
prep_maker.sh		prep_maker.sh
prep_ref.sh		prep_ref.sh
run_AGAPE.sh		run_AGAPE.sh
run_AGAPE_per_seq.sh		run_AGAPE_per_seq.sh
run_agape_assembly.sh		run_agape_assembly.sh
run_comb_annot.sh		run_comb_annot.sh
run_hugeseq.sh		run_hugeseq.sh
run_maker.sh		run_maker.sh
run_non_ref.sh		run_non_ref.sh
test.sh		test.sh
unannot_regions.sh		unannot_regions.sh
yeast_reference.tar.gz		yeast_reference.tar.gz

yeastgenome/AGAPE

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