Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

PR dev - PBSIM replaces NANOSIM, new version 0.4.0 #57

Merged
merged 9 commits into from
Jun 7, 2024
Merged

PR dev - PBSIM replaces NANOSIM, new version 0.4.0 #57

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
5970bc9
Update README.md
Krannich479 May 30, 2024
d3ea138
Update README.md
Krannich479 May 30, 2024
e4599ab
Update main.nf
Krannich479 Jun 4, 2024
91fcf0d
update gitignore
Krannich479 Jun 7, 2024
4fb4432
Merge branch 'dev' of https://github.com/rki-mf1/cievad into HEAD
Krannich479 Jun 7, 2024
496c147
update README
Krannich479 Jun 7, 2024
2615a85
update README
Krannich479 Jun 7, 2024
2142321
PBSIM replaces NANOSIM in default setup; added latest nanosim model; …
Krannich479 Jun 7, 2024
b5d544e
bump new version 0.4.0
Krannich479 Jun 7, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 6 additions & 2 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,8 @@ bin/*
!bin/mason_simulator
!bin/SURVIVOR
!bin/amplisim-v0_1_0-ubuntu_20_04
!bin/pbsim


data/*
data-ci/*
Expand All @@ -10,10 +12,12 @@ logs/*

.snakemake/

reference/

configs/

databases/

singularity_images/

results/

aux/nanosim_model/human_NA12878_DNA_FAB49712_guppy.tar.gz
Expand Down
2 changes: 1 addition & 1 deletion VERSION
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1 +1 @@
'0.3.1'
'0.4.0'
Binary file added aux/nanosim_model/human_giab_hg002_sub1M_kitv14_dorado/hg002_nanosim_sub1M_aligned_reads.pkl
View file
Open in desktop
Binary file not shown.
Binary file added ...nanosim_model/human_giab_hg002_sub1M_kitv14_dorado/hg002_nanosim_sub1M_aligned_region.pkl
View file
Open in desktop
Binary file not shown.
1 change: 1 addition & 0 deletions aux/nanosim_model/human_giab_hg002_sub1M_kitv14_dorado/hg002_nanosim_sub1M_chimeric_info
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
Mean segments for each aligned read: 1.0487833720837008
8 changes: 8 additions & 0 deletions ...nanosim_model/human_giab_hg002_sub1M_kitv14_dorado/hg002_nanosim_sub1M_error_markov_model
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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
4 changes: 4 additions & 0 deletions aux/nanosim_model/human_giab_hg002_sub1M_kitv14_dorado/hg002_nanosim_sub1M_error_rate.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
Mismatch rate: 0.007370052148345708
Insertion rate: 0.005280295851015525
Deletion rate: 0.007241469288345598
Total error rate: 0.01989181728770683
Loading