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[update] distance populations for conference figures
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@LaraFuhrmann
LaraFuhrmann committed Nov 13, 2023
1 parent e0f8817 commit 4d79916
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5 changes: 3 additions & 2 deletions ...auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/config.yaml
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method_list: [lofreq_local_haplo,
shorah_default,
cliquesnv_local_haplo,
cliquesnv_local_haplo_snv,
#cliquesnv_local_haplo,
#cliquesnv_local_haplo_snv,
cliquesnv_local_haplo_tf0.01,
cliquesnv_local_haplo_snv_tf0.01,
viloca_alpha_0.000001,
viloca_alpha_0.000001_K300,
viloca_alpha_0.00001,
viloca_alpha_0.00001_K100,
viloca_multi,
# shorah_default_amplicon, --> here the short illumina simulation still not work due to b2w errors
]
replicate_count: 5
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86 changes: 45 additions & 41 deletions .../auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/params.csv
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seq_tech,seq_mode,seq_mode_param,read_length,genome_size,coverage,haplos
# Population 1
illumina,shotgun,single_amplicon,249,249,1000,2@3@30@20@20@[email protected]
illumina,shotgun,single_amplicon,201,201,1000,2@3@30@20@20@[email protected]
#illumina,shotgun,single_amplicon,201,201,1000,2@3@30@20@20@[email protected]
# Population 2
illumina,shotgun,single_amplicon,249,249,1000,5@5@20@4@12@[email protected]
illumina,shotgun,single_amplicon,201,201,1000,5@5@20@4@15@[email protected]
#illumina,shotgun,single_amplicon,201,201,1000,5@5@20@4@15@[email protected]
# Population 3 (vary covverage)
illumina,shotgun,single_amplicon,249,249,100,5@5@30@10@15@[email protected]
illumina,shotgun,single_amplicon,249,249,500,5@5@30@10@15@[email protected]
illumina,shotgun,single_amplicon,249,249,800,5@5@30@10@15@[email protected]
illumina,shotgun,single_amplicon,249,249,1000,5@5@30@10@15@[email protected]
illumina,shotgun,single_amplicon,249,249,5000,5@5@30@10@15@[email protected]
illumina,shotgun,single_amplicon,249,249,10000,5@5@30@10@15@[email protected]
illumina,shotgun,single_amplicon,201,201,100,5@5@30@10@15@[email protected]
illumina,shotgun,single_amplicon,201,201,500,5@5@30@10@15@[email protected]
illumina,shotgun,single_amplicon,201,201,800,5@5@30@10@15@[email protected]
illumina,shotgun,single_amplicon,201,201,1000,5@5@30@10@15@[email protected]
illumina,shotgun,single_amplicon,201,201,5000,5@5@30@10@15@[email protected]
illumina,shotgun,single_amplicon,201,201,10000,5@5@30@10@15@[email protected]
#illumina,shotgun,single_amplicon,201,201,100,5@5@30@10@15@[email protected]
#illumina,shotgun,single_amplicon,201,201,500,5@5@30@10@15@[email protected]
#illumina,shotgun,single_amplicon,201,201,800,5@5@30@10@15@[email protected]
#illumina,shotgun,single_amplicon,201,201,1000,5@5@30@10@15@[email protected]
#illumina,shotgun,single_amplicon,201,201,5000,5@5@30@10@15@[email protected]
#illumina,shotgun,single_amplicon,201,201,10000,5@5@30@10@15@[email protected]
# Population 4
illumina,shotgun,single_amplicon,201,201,1000,5@10@30@10@10@[email protected]
illumina,shotgun,single_amplicon,249,249,1000,5@10@30@10@10@[email protected]
illumina,shotgun,single_amplicon,201,201,1000,5@10@30@10@15@[email protected]
#illumina,shotgun,single_amplicon,201,201,1000,5@10@30@10@10@[email protected]
#illumina,shotgun,single_amplicon,249,249,1000,5@10@30@10@10@[email protected]
#illumina,shotgun,single_amplicon,201,201,1000,5@10@30@10@15@[email protected]
illumina,shotgun,single_amplicon,249,249,1000,5@10@30@10@15@[email protected]
# Population 5
illumina,shotgun,single_amplicon,249,249,1000,5@15@30@10@15@[email protected]
illumina,shotgun,single_amplicon,201,201,1000,5@15@30@10@15@[email protected]
#illumina,shotgun,single_amplicon,201,201,1000,5@15@30@10@15@[email protected]
# Population 6
nanopore,shotgun,single_amplicon,5000,5000,800,2@3@600@400@400@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,2000,2@3@600@400@400@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,800,2@3@600@400@400@[email protected] ## I decided to go for coverage = 1000 as baseline for long read seq
#nanopore,shotgun,single_amplicon,5000,5000,2000,2@3@600@400@400@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,1000,2@3@600@400@400@[email protected]
#pacbio,shotgun,single_amplicon,5000,5000,1000,2@3@600@400@400@[email protected]
# Population 7
nanopore,shotgun,single_amplicon,5000,5000,800,5@5@400@80@240@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,2000,5@5@400@80@240@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@400@80@240@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,800,5@5@400@80@200@[email protected]
pacbio,shotgun,single_amplicon,5000,5000,1000,2@3@600@400@400@[email protected]
# Population 6 - easy
nanopore,shotgun,single_amplicon,5000,5000,1000,2@3@600@600@600@[email protected]
pacbio,shotgun,single_amplicon,5000,5000,1000,2@3@600@600@600@[email protected]
# Population 7 (too difficult --> exclude )
#nanopore,shotgun,single_amplicon,5000,5000,800,5@5@400@80@240@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,2000,5@5@400@80@240@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@400@80@240@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,800,5@5@400@80@200@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,2000,5@5@400@80@200@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@400@80@200@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@400@80@200@[email protected]
#pacbio,shotgun,single_amplicon,5000,5000,1000,5@5@400@80@240@[email protected]
# Population 8 (vary coverage)
nanopore,shotgun,single_amplicon,5000,5000,100,5@5@600@200@300@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,200,5@5@600@200@300@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,500,5@5@600@200@300@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,800,5@5@600@200@300@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@600@200@300@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,5000,5@5@600@200@300@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,100,5@5@600@200@240@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,200,5@5@600@200@240@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,500,5@5@600@200@240@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,800,5@5@600@200@240@[email protected]
# Population 8 (vary coverage --> not yet for conference, focus on conference)
#nanopore,shotgun,single_amplicon,5000,5000,100,5@5@600@200@300@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,200,5@5@600@200@300@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,500,5@5@600@200@300@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,800,5@5@600@200@300@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@600@200@300@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,5000,5@5@600@200@300@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,100,5@5@600@200@240@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,200,5@5@600@200@240@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,500,5@5@600@200@240@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,800,5@5@600@200@240@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@600@200@240@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,5000,5@5@600@200@240@[email protected]
pacbio,shotgun,single_amplicon,5000,5000,1000,5@5@600@200@240@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,5000,5@5@600@200@240@[email protected]
#pacbio,shotgun,single_amplicon,5000,5000,100,5@5@600@200@300@[email protected]
#pacbio,shotgun,single_amplicon,5000,5000,200,5@5@600@200@300@[email protected]
#pacbio,shotgun,single_amplicon,5000,5000,500,5@5@600@200@300@[email protected]
#pacbio,shotgun,single_amplicon,5000,5000,800,5@5@600@200@300@[email protected]
#pacbio,shotgun,single_amplicon,5000,5000,1000,5@5@600@200@300@[email protected]
#pacbio,shotgun,single_amplicon,5000,5000,5000,5@5@600@200@300@[email protected]
# Population 9
nanopore,shotgun,single_amplicon,5000,5000,800,5@10@600@200@300@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,2000,5@10@600@200@300@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@300@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,800,5@10@600@200@240@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,2000,5@10@600@200@240@[email protected]
nanopore,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@240@[email protected]
# Population 9 (show but say look how bad this gets with more haplotypes)
#nanopore,shotgun,single_amplicon,5000,5000,800,5@10@600@200@300@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,2000,5@10@600@200@300@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@300@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,800,5@10@600@200@240@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,2000,5@10@600@200@240@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@240@[email protected]
#pacbio,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@300@[email protected]
# Population 10
# Population 10 (too difficult for long read seq data)
#nanopore,shotgun,single_amplicon,5000,5000,800,15@5@600@300@200@[email protected] --> coverage_haplotype 0
#nanopore,shotgun,single_amplicon,5000,5000,5000,15@5@600@300@200@[email protected]
#nanopore,shotgun,single_amplicon,5000,5000,1000,15@5@600@300@200@[email protected]
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