Merge pull request #57 from rki-mf1/dev

PR dev - PBSIM replaces NANOSIM, new version 0.4.0
rki-mf1 · Jun 7, 2024 · 64ac2fc · 64ac2fc
2 parents 5224b61 + b5d544e
commit 64ac2fc
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Showing 24 changed files with 21,414 additions and 32 deletions.
diff --git a/.gitignore b/.gitignore
@@ -2,6 +2,8 @@ bin/*
 !bin/mason_simulator
 !bin/SURVIVOR
 !bin/amplisim-v0_1_0-ubuntu_20_04
+!bin/pbsim
+
 
 data/*
 data-ci/*
@@ -10,10 +12,12 @@ logs/*
 
 .snakemake/
 
-reference/
-
 configs/
 
+databases/
+
+singularity_images/
+
 results/
 
 aux/nanosim_model/human_NA12878_DNA_FAB49712_guppy.tar.gz

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-'0.3.1'
+'0.4.0'
diff --git a/aux/nanosim_model/human_giab_hg002_sub1M_kitv14_dorado/hg002_nanosim_sub1M_aligned_reads.pkl b/aux/nanosim_model/human_giab_hg002_sub1M_kitv14_dorado/hg002_nanosim_sub1M_aligned_reads.pkl
diff --git a/...nanosim_model/human_giab_hg002_sub1M_kitv14_dorado/hg002_nanosim_sub1M_aligned_region.pkl b/...nanosim_model/human_giab_hg002_sub1M_kitv14_dorado/hg002_nanosim_sub1M_aligned_region.pkl
diff --git a/aux/nanosim_model/human_giab_hg002_sub1M_kitv14_dorado/hg002_nanosim_sub1M_chimeric_info b/aux/nanosim_model/human_giab_hg002_sub1M_kitv14_dorado/hg002_nanosim_sub1M_chimeric_info
@@ -0,0 +1 @@
+Mean segments for each aligned read:	1.0487833720837008
diff --git a/...nanosim_model/human_giab_hg002_sub1M_kitv14_dorado/hg002_nanosim_sub1M_error_markov_model b/...nanosim_model/human_giab_hg002_sub1M_kitv14_dorado/hg002_nanosim_sub1M_error_markov_model
@@ -0,0 +1,8 @@
+succedent 	mis	ins	del
+start	0.3667695682590252	0.2834764459999186	0.3497539857410562
+mis	0.5128689406805294	0.21642594955734523	0.2707051097621255
+ins	0.40725764797898556	0.2805410906739999	0.3122012613470145
+del	0.41078824731713565	0.23840499549388153	0.35080675718898285
+mis0	0.0	0.33783783783783783	0.6621621621621622
+ins0	0.9999333356943608	0.0	6.666430563917528e-05
+del0	0.9999835183159985	1.6481684001520192e-05	0.0
diff --git a/aux/nanosim_model/human_giab_hg002_sub1M_kitv14_dorado/hg002_nanosim_sub1M_error_rate.tsv b/aux/nanosim_model/human_giab_hg002_sub1M_kitv14_dorado/hg002_nanosim_sub1M_error_rate.tsv
@@ -0,0 +1,4 @@
+Mismatch rate:	0.007370052148345708
+Insertion rate:	0.005280295851015525
+Deletion rate:	0.007241469288345598
+Total error rate:	0.01989181728770683
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Mean segments for each aligned read: 1.0487833720837008