neherlab/pangraph-0.6.3.zip
neherlab-pangraph-6aa83e7
.dockerignore
202 Bytes
.env
31 Bytes
.gitattributes
126 Bytes
.github
workflows
build.yml
1.9 kB
docs.yml
835 Bytes
.gitignore
421 Bytes
CHANGELOG.md
4.3 kB
Dockerfile
2.0 kB
LICENSE
1.1 kB
Makefile
2.9 kB
Manifest.toml
13.9 kB
Project.toml
1.0 kB
README.md
5.1 kB
bin
setup-pangraph
1.6 kB
compile.jl
253 Bytes
deps
minimap2
Makefile
99 Bytes
build_tarballs.jl
758 Bytes
static
patches
Makefile.diff
431 Bytes
docs
make.jl
1.3 kB
src
assets
alignment_scheme.png
277.4 kB
bandage_ecoli_full.png
200.7 kB
dgenies_dotplot.png
735.9 kB
ecoli_blockstats.png
44.2 kB
klebs_full_pangraph.png
84.8 kB
klebs_marginal_pangraph.png
38.2 kB
kpc_graph.png
484.0 kB
linear_and_graph_kpc.png
333.3 kB
pangraph_inversion.png
38.0 kB
pangraph_scheme.png
139.9 kB
panx_visualization.png
419.3 kB
plasmid_example_pangraph.png
66.4 kB
plasmid_example_pangraph_linear.png
422.1 kB
cli
build.md
2.4 kB
export.md
2.9 kB
generate.md
1.5 kB
marginalize.md
1.4 kB
polish.md
938 Bytes
version.md
156 Bytes
dev
building-docker.md
1.6 kB
building-documentation.md
1.3 kB
releasing.md
2.9 kB
index.md
10.3 kB
lib
align.md
185 Bytes
block.md
184 Bytes
edge.md
180 Bytes
gfa.md
174 Bytes
graph.md
190 Bytes
mash.md
193 Bytes
minimap.md
182 Bytes
mmseqs.md
178 Bytes
node.md
181 Bytes
pangraph.md
165 Bytes
path.md
180 Bytes
simulate.md
182 Bytes
utility.md
186 Bytes
tutorials
tutorial_1.md
7.1 kB
tutorial_2.md
11.9 kB
tutorial_3.md
7.4 kB
tutorial_4.md
5.2 kB
tutorial_5.md
5.7 kB
tutorial_6.md
5.6 kB
example_datasets
ecoli.fa.gz
15.3 MB
klebs.fa.gz
14.8 MB
script
Manifest.toml
46.7 kB
Project.toml
1.1 kB
README.md
3.2 kB
Snakefile
194 Bytes
cluster
cluster_config.json
1.3 kB
config.yaml
286 Bytes
slurm_submit.sh
331 Bytes
conda_envs
bioinfo_env.yml
4.1 kB
pangraph_build_env.yml
1.1 kB
config
accession_numbers.csv
7.5 kB
accnums.json
12.8 kB
accuracy_sim_params.json
791 Bytes
config.yml
927 Bytes
incremental_size_strains.json
69.5 kB
marginalize_pairs.csv
10.9 kB
projection_strains.json
27.7 kB
size_benchmark_sim_params.json
215 Bytes
pick_strain_sets.py
3.6 kB
rules
accuracy.smk
6.3 kB
marginalization.smk
7.5 kB
panx.smk
10.2 kB
paper_figs.smk
4.8 kB
size_benchmark.smk
3.4 kB
src
PanGraphScripts.jl
70 Bytes
workflow_scripts
compression_benchmark.py
3.8 kB
compression_summary.py
4.7 kB
concatenate-database.jl
274 Bytes
gbk_to_fa.py
1.6 kB
incr_size_extract_stats.py
3.4 kB
incr_size_summary_df.py
2.1 kB
make-accuracy.jl
7.3 kB
make-sequence.jl
987 Bytes
pairwise_vs_marginalize.jl
7.4 kB
pairwise_vs_marginalize_example.py
4.8 kB
pairwise_vs_marginalize_summary.py
4.8 kB
panx_dataset_diversity.py
7.1 kB
panx_dataset_diversity_averages.py
2.2 kB
panx_pairwise_core_divergence.py
4.3 kB
paper_figs
accuracy_plot_utils.py
10.6 kB
accuracy_plots.py
5.1 kB
accuracy_to_json.jl
1.0 kB
incremental_size_plot.py
4.7 kB
panx_benchmark_plot.py
10.0 kB
projections_plot.py
3.8 kB
projections_plot_single.py
5.1 kB
synthetic_data_benchmark.py
4.1 kB
plot-accuracy-comparison.jl
5.2 kB
plot-accuracy.jl
5.1 kB
shared_kmers_pair.py
2.0 kB
size_benchmark_summary_dataframe.py
2.3 kB
size_benchmark_summary_plot.py
2.8 kB
summary_benchmark.py
4.3 kB
src
PanGraph.jl
3.4 kB
align.jl
20.2 kB
args.jl
5.1 kB
block.jl
50.5 kB
build.jl
4.8 kB
cmd.jl
2.1 kB
counter.jl
172 Bytes
edge.jl
9.9 kB
export.jl
5.2 kB
generate.jl
2.8 kB
gfa.jl
4.9 kB
graph.jl
20.1 kB
help.jl
482 Bytes
interval.jl
7.9 kB
junction.jl
1.6 kB
marginalize.jl
2.9 kB
mash.jl
6.5 kB
minimap.jl
9.3 kB
mmseqs.jl
2.0 kB
node.jl
1.3 kB
panX.jl
9.2 kB
path.jl
8.6 kB
polish.jl
1.3 kB
pool.jl
3.2 kB
simulate.jl
10.8 kB
static
watson-crick.jl
931 Bytes
util.jl
21.1 kB
version.jl
542 Bytes
tests
run-cli-tests.sh
2.0 kB
tools
extract_release_notes.py
1.1 kB
release.sh
3.0 kB
release_checks.py
3.4 kB
trace.jl
1.1 kB