From 4d799161a457f851a9a38a7db3e1a074bd4a0ea8 Mon Sep 17 00:00:00 2001 From: LaraFuhrmann <55209716+LaraFuhrmann@users.noreply.github.com> Date: Mon, 13 Nov 2023 16:14:49 +0100 Subject: [PATCH] [update] distance populations for conference figures --- .../config_distance/config.yaml | 5 +- .../config_distance/params.csv | 86 ++++++++++--------- 2 files changed, 48 insertions(+), 43 deletions(-) diff --git a/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/config.yaml b/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/config.yaml index 15fb1782..6765084a 100644 --- a/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/config.yaml +++ b/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/config.yaml @@ -1,13 +1,14 @@ 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 diff --git a/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/params.csv b/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/params.csv index de190433..80f49b63 100644 --- a/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/params.csv +++ b/resources/auxiliary_workflows/benchmark/resources/local_haplotype_setup/config_distance/params.csv @@ -1,10 +1,10 @@ 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@geom@0.75 -illumina,shotgun,single_amplicon,201,201,1000,2@3@30@20@20@geom@0.75 +#illumina,shotgun,single_amplicon,201,201,1000,2@3@30@20@20@geom@0.75 # Population 2 illumina,shotgun,single_amplicon,249,249,1000,5@5@20@4@12@geom@0.75 -illumina,shotgun,single_amplicon,201,201,1000,5@5@20@4@15@geom@0.75 +#illumina,shotgun,single_amplicon,201,201,1000,5@5@20@4@15@geom@0.75 # Population 3 (vary covverage) illumina,shotgun,single_amplicon,249,249,100,5@5@30@10@15@geom@0.75 illumina,shotgun,single_amplicon,249,249,500,5@5@30@10@15@geom@0.75 @@ -12,61 +12,65 @@ illumina,shotgun,single_amplicon,249,249,800,5@5@30@10@15@geom@0.75 illumina,shotgun,single_amplicon,249,249,1000,5@5@30@10@15@geom@0.75 illumina,shotgun,single_amplicon,249,249,5000,5@5@30@10@15@geom@0.75 illumina,shotgun,single_amplicon,249,249,10000,5@5@30@10@15@geom@0.75 -illumina,shotgun,single_amplicon,201,201,100,5@5@30@10@15@geom@0.75 -illumina,shotgun,single_amplicon,201,201,500,5@5@30@10@15@geom@0.75 -illumina,shotgun,single_amplicon,201,201,800,5@5@30@10@15@geom@0.75 -illumina,shotgun,single_amplicon,201,201,1000,5@5@30@10@15@geom@0.75 -illumina,shotgun,single_amplicon,201,201,5000,5@5@30@10@15@geom@0.75 -illumina,shotgun,single_amplicon,201,201,10000,5@5@30@10@15@geom@0.75 +#illumina,shotgun,single_amplicon,201,201,100,5@5@30@10@15@geom@0.75 +#illumina,shotgun,single_amplicon,201,201,500,5@5@30@10@15@geom@0.75 +#illumina,shotgun,single_amplicon,201,201,800,5@5@30@10@15@geom@0.75 +#illumina,shotgun,single_amplicon,201,201,1000,5@5@30@10@15@geom@0.75 +#illumina,shotgun,single_amplicon,201,201,5000,5@5@30@10@15@geom@0.75 +#illumina,shotgun,single_amplicon,201,201,10000,5@5@30@10@15@geom@0.75 # Population 4 -illumina,shotgun,single_amplicon,201,201,1000,5@10@30@10@10@geom@0.75 -illumina,shotgun,single_amplicon,249,249,1000,5@10@30@10@10@geom@0.75 -illumina,shotgun,single_amplicon,201,201,1000,5@10@30@10@15@geom@0.75 +#illumina,shotgun,single_amplicon,201,201,1000,5@10@30@10@10@geom@0.75 +#illumina,shotgun,single_amplicon,249,249,1000,5@10@30@10@10@geom@0.75 +#illumina,shotgun,single_amplicon,201,201,1000,5@10@30@10@15@geom@0.75 illumina,shotgun,single_amplicon,249,249,1000,5@10@30@10@15@geom@0.75 # Population 5 illumina,shotgun,single_amplicon,249,249,1000,5@15@30@10@15@geom@0.75 -illumina,shotgun,single_amplicon,201,201,1000,5@15@30@10@15@geom@0.75 +#illumina,shotgun,single_amplicon,201,201,1000,5@15@30@10@15@geom@0.75 # Population 6 -nanopore,shotgun,single_amplicon,5000,5000,800,2@3@600@400@400@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,2000,2@3@600@400@400@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,800,2@3@600@400@400@geom@0.75 ## 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@geom@0.75 nanopore,shotgun,single_amplicon,5000,5000,1000,2@3@600@400@400@geom@0.75 -#pacbio,shotgun,single_amplicon,5000,5000,1000,2@3@600@400@400@geom@0.75 -# Population 7 -nanopore,shotgun,single_amplicon,5000,5000,800,5@5@400@80@240@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,2000,5@5@400@80@240@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@400@80@240@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,800,5@5@400@80@200@geom@0.75 +pacbio,shotgun,single_amplicon,5000,5000,1000,2@3@600@400@400@geom@0.75 +# Population 6 - easy +nanopore,shotgun,single_amplicon,5000,5000,1000,2@3@600@600@600@geom@0.75 +pacbio,shotgun,single_amplicon,5000,5000,1000,2@3@600@600@600@geom@0.75 +# Population 7 (too difficult --> exclude ) +#nanopore,shotgun,single_amplicon,5000,5000,800,5@5@400@80@240@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,2000,5@5@400@80@240@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@400@80@240@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,800,5@5@400@80@200@geom@0.75 #nanopore,shotgun,single_amplicon,5000,5000,2000,5@5@400@80@200@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@400@80@200@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@400@80@200@geom@0.75 #pacbio,shotgun,single_amplicon,5000,5000,1000,5@5@400@80@240@geom@0.75 -# Population 8 (vary coverage) -nanopore,shotgun,single_amplicon,5000,5000,100,5@5@600@200@300@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,200,5@5@600@200@300@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,500,5@5@600@200@300@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,800,5@5@600@200@300@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@600@200@300@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,5000,5@5@600@200@300@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,100,5@5@600@200@240@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,200,5@5@600@200@240@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,500,5@5@600@200@240@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,800,5@5@600@200@240@geom@0.75 +# Population 8 (vary coverage --> not yet for conference, focus on conference) +#nanopore,shotgun,single_amplicon,5000,5000,100,5@5@600@200@300@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,200,5@5@600@200@300@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,500,5@5@600@200@300@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,800,5@5@600@200@300@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@600@200@300@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,5000,5@5@600@200@300@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,100,5@5@600@200@240@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,200,5@5@600@200@240@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,500,5@5@600@200@240@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,800,5@5@600@200@240@geom@0.75 nanopore,shotgun,single_amplicon,5000,5000,1000,5@5@600@200@240@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,5000,5@5@600@200@240@geom@0.75 +pacbio,shotgun,single_amplicon,5000,5000,1000,5@5@600@200@240@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,5000,5@5@600@200@240@geom@0.75 #pacbio,shotgun,single_amplicon,5000,5000,100,5@5@600@200@300@geom@0.75 #pacbio,shotgun,single_amplicon,5000,5000,200,5@5@600@200@300@geom@0.75 #pacbio,shotgun,single_amplicon,5000,5000,500,5@5@600@200@300@geom@0.75 #pacbio,shotgun,single_amplicon,5000,5000,800,5@5@600@200@300@geom@0.75 #pacbio,shotgun,single_amplicon,5000,5000,1000,5@5@600@200@300@geom@0.75 #pacbio,shotgun,single_amplicon,5000,5000,5000,5@5@600@200@300@geom@0.75 -# Population 9 -nanopore,shotgun,single_amplicon,5000,5000,800,5@10@600@200@300@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,2000,5@10@600@200@300@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@300@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,800,5@10@600@200@240@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,2000,5@10@600@200@240@geom@0.75 -nanopore,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@240@geom@0.75 +# 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@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,2000,5@10@600@200@300@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@300@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,800,5@10@600@200@240@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,2000,5@10@600@200@240@geom@0.75 +#nanopore,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@240@geom@0.75 #pacbio,shotgun,single_amplicon,5000,5000,1000,5@10@600@200@300@geom@0.75 -# Population 10 +# Population 10 (too difficult for long read seq data) #nanopore,shotgun,single_amplicon,5000,5000,800,15@5@600@300@200@geom@0.75 --> coverage_haplotype 0 #nanopore,shotgun,single_amplicon,5000,5000,5000,15@5@600@300@200@geom@0.75 #nanopore,shotgun,single_amplicon,5000,5000,1000,15@5@600@300@200@geom@0.75