fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-02 20:28:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

better parameters for short reads

Browse Source 
It turns out the key problem is not the minimizer density. It is the max
occurrence that tends to affect results more, especially sensitivity. There is
still lots of work to do, but for now, it seems a good start.
This commit is contained in:
Heng Li
2017-09-12 16:11:23 -04:00
parent eea9e851d8
commit d7f2ac1d4f
3 changed files with 13 additions and 6 deletions
Download Patch File Download Diff File Expand all files Collapse all files
main.c
+8 -6
View File
@@ -156,17 +156,19 @@ int main(int argc, char *argv[])
k = 19, w = 19;
opt.a = 1, opt.b = 9, opt.q = 16, opt.q2 = 41, opt.e = 2, opt.e2 = 1, opt.zdrop = 200;
opt.min_dp_max = 200;
} else if (strcmp(optarg, "short") == 0) {
k = 17, w = 7, is_hpc = 0;
} else if (strcmp(optarg, "short") == 0 || strcmp(optarg, "sr") == 0) {
k = 21, w = 11, is_hpc = 0;
minibatch_size = 50000000;
opt.flag |= MM_F_SR;
opt.a = 2, opt.b = 8, opt.q = 12, opt.e = 2, opt.q2 = 32, opt.e2 = 1;
opt.max_gap = 100;
opt.pri_ratio = 0.5f;
opt.min_cnt = 2;
opt.min_chain_score = 20;
opt.min_dp_max = 50;
opt.best_n = 10;
opt.bw = 100;
opt.mid_occ_frac = 1e-4f;
opt.min_dp_max = 40;
opt.best_n = 20;
opt.bw = 50;
opt.mid_occ_frac = 2e-5f;
} else if (strcmp(optarg, "splice") == 0 || strcmp(optarg, "cdna") == 0) {
k = 15, w = 5;
opt.flag |= MM_F_SPLICE | MM_F_SPLICE_FOR | MM_F_SPLICE_REV;