Optimize parameters

[marcelm]

Here are the results from the parameter optimization script for all read lengths, run on the multi-context seeds branch.

How the script was run

For reproducibility, I plan to make the script publicly available at https://github.com/NBISweden/strobealign-evaluation.

I ran it on strobealign commit c4a7f61 (from PR #388). This was the command:

for r in 50 75 100 150 200 300 500; do
    ./search.py -c c4a7f61 -x -r $r --mapping-rate-slack 1
done

• --mapping-rate-slack 1 means that all parameter combinations are skipped for which the mapping rate of one of the datasets is reduced by more than 1 percentage points.
• -x means that accuracy for mapping-only mode is optimized (i.e., running strobealign with -x). However, when the list of parameters has been found, the script reports also results for extension-alignment mode so that one can check how its accuracies change.

Suggested changes

Parameters are given as a tuple $(k, s, l, u)$.

Canonical read length	Before	Suggestion
50	(18, 14, -2, 1)	(18, 14, -2, 1) -- No change
75	(20, 16, -3, 2)	(20, 16, -3, 2) -- No change[^1]
100	(20, 16, -2, 2)	(19, 15, 0, 3) or maybe (18, 14, 1, 3)
125	(20, 16, -1, 4)	not measured
150	(20, 16, 1, 7)	(21, 17, 2, 6)
250	(22, 18, 2, 12)	(22, 18, 4, 13)
400	(23, 17, 2, 12)	(24, 18, 6, 13)

I am unsure about read length 75 and 100: With these new settings, $k$ would decrease when going from read length 75 to 100, which is a bit unexpected.

[^1]: Already added as new canonical read length

Detailed results

## Read length 50: Weighted SE/PE results - mapping-only ``` parameters acc_se acc_pe diff_se diff_pe mprt_se mprt_pe diff_se diff_pe (16, 12, -2, -1) 63.4387 75.2934 +0.5503 +1.0594 96.121 96.112 -0.855 -0.864 (16, 12, -2, 0) 63.2349 74.9216 +0.3466 +0.6877 97.123 97.112 +0.146 +0.136 (16, 12, -2, 1) 63.2007 74.8490 +0.3124 +0.6150 97.252 97.244 +0.275 +0.268 (16, 12, -2, 2) 63.1981 74.8449 +0.3097 +0.6110 97.254 97.246 +0.277 +0.270 (17, 13, -2, 0) 63.1308 74.6860 +0.2425 +0.4520 96.977 96.969 -0.000 -0.007 (17, 13, -2, 1) 63.0462 74.5605 +0.1578 +0.3265 97.151 97.143 +0.174 +0.168 (17, 13, -2, 2) 63.0538 74.5557 +0.1654 +0.3218 97.158 97.150 +0.181 +0.174 (18, 14, -2, 0) 62.9883 74.4344 +0.0999 +0.2004 96.756 96.754 -0.220 -0.222 (18, 14, -2, 1) 62.8884 74.2339 +0.0000 +0.0000 96.977 96.976 +0.000 +0.000 ***** (18, 14, -2, 2) 62.8892 74.2215 +0.0008 -0.0124 96.992 96.992 +0.015 +0.016 (19, 15, -2, 0) 62.7956 74.0796 -0.0927 -0.1543 96.444 96.435 -0.532 -0.541 (19, 15, -2, 1) 62.6517 73.8086 -0.2366 -0.4253 96.693 96.682 -0.284 -0.294 (19, 15, -2, 2) 62.6419 73.7709 -0.2465 -0.4630 96.711 96.700 -0.266 -0.276 (20, 16, -3, -1) 62.5432 73.7019 -0.3451 -0.5320 95.983 95.981 -0.993 -0.995 (20, 16, -3, 0) 62.3455 73.3375 -0.5429 -0.8964 96.256 96.254 -0.720 -0.722 (20, 16, -3, 2) 62.3125 73.2746 -0.5759 -0.9593 96.287 96.287 -0.690 -0.689 ``` ## Read length 50: Weighted SE/PE results - with extension alignment ``` parameters sacc_se sacc_pe diff_se diff_pe acc_se acc_pe diff_se diff_pe mprt_se mprt_pe diff_se diff_pe (17, 13, -2, 2) 93.2023 97.3829 +0.1056 -0.0185 66.0838 80.8513 +0.2597 +0.0863 97.158 99.540 +0.181 -0.025 (17, 13, -2, 1) 93.1958 97.3838 +0.0991 -0.0175 66.0857 80.8555 +0.2617 +0.0904 97.151 99.538 +0.174 -0.027 (18, 14, -2, 1) 93.0968 97.4014 +0.0000 +0.0000 65.8240 80.7651 +0.0000 +0.0000 96.977 99.565 +0.000 +0.000 ***** (16, 12, -2, 2) 93.2631 97.3571 +0.1664 -0.0443 66.3198 80.8874 +0.4958 +0.1223 97.254 99.523 +0.277 -0.042 (18, 14, -2, 2) 93.1042 97.3955 +0.0074 -0.0058 65.8092 80.7592 -0.0148 -0.0059 96.992 99.569 +0.015 +0.004 (16, 12, -2, 1) 93.2566 97.3568 +0.1598 -0.0446 66.3178 80.8901 +0.4938 +0.1251 97.252 99.523 +0.275 -0.042 (17, 13, -2, 0) 93.0792 97.3695 -0.0176 -0.0319 66.1453 80.9034 +0.3213 +0.1384 96.977 99.489 -0.000 -0.076 (16, 12, -2, 0) 93.1696 97.3440 +0.0728 -0.0574 66.3488 80.9302 +0.5248 +0.1651 97.123 99.487 +0.146 -0.077 (18, 14, -2, 0) 92.9687 97.3935 -0.1281 -0.0079 65.9244 80.8640 +0.1003 +0.0990 96.756 99.503 -0.220 -0.062 (19, 15, -2, 1) 92.8954 97.3900 -0.2013 -0.0113 65.5049 80.6756 -0.3192 -0.0894 96.693 99.582 -0.284 +0.017 (19, 15, -2, 2) 92.9051 97.3837 -0.1917 -0.0177 65.4790 80.6566 -0.3450 -0.1084 96.711 99.588 -0.266 +0.023 (19, 15, -2, 0) 92.7360 97.3945 -0.3607 -0.0069 65.6364 80.8018 -0.1876 +0.0367 96.444 99.518 -0.532 -0.047 (20, 16, -3, 0) 92.5362 97.3404 -0.5606 -0.0610 65.1052 80.5565 -0.7189 -0.2086 96.256 99.557 -0.720 -0.008 (20, 16, -3, 2) 92.5494 97.3297 -0.5474 -0.0716 65.0667 80.5175 -0.7573 -0.2475 96.287 99.565 -0.690 +0.000 (20, 16, -3, -1) 92.3606 97.3623 -0.7362 -0.0390 65.2622 80.7295 -0.5618 -0.0355 95.983 99.482 -0.993 -0.083 (16, 12, -2, -1) 92.6051 97.1949 -0.4917 -0.2065 66.5108 81.0825 +0.6868 +0.3174 96.121 99.136 -0.855 -0.429 ``` ## Read length 75: Weighted SE/PE results - mapping-only ``` parameters acc_se acc_pe diff_se diff_pe mprt_se mprt_pe diff_se diff_pe (21, 17, -3, -1) 71.7299 82.5870 +0.0342 +0.0823 98.887 98.888 -0.258 -0.260 (20, 16, -3, 0) 71.6998 82.5136 +0.0042 +0.0089 99.119 99.123 -0.025 -0.025 (20, 16, -3, 1) 71.6971 82.5044 +0.0015 -0.0003 99.144 99.148 -0.000 -0.000 (20, 16, -3, 2) 71.6957 82.5047 +0.0000 -0.0000 99.145 99.149 +0.000 +0.000 ***** (20, 16, -3, 3) 71.6957 82.5047 +0.0000 -0.0000 99.145 99.149 +0.000 +0.000 (18, 14, -2, 1) 71.4264 82.4369 -0.2693 -0.0678 99.043 99.044 -0.102 -0.105 ``` ## Read length 75: Weighted SE/PE results - with extension alignment ``` parameters sacc_se sacc_pe diff_se diff_pe acc_se acc_pe diff_se diff_pe mprt_se mprt_pe diff_se diff_pe (20, 16, -3, 2) 95.9650 98.4305 +0.0000 +0.0000 74.9245 86.7311 +0.0000 +0.0000 99.145 99.792 +0.000 -0.000 ***** (20, 16, -3, 3) 95.9650 98.4305 +0.0000 +0.0000 74.9245 86.7311 +0.0000 +0.0000 99.145 99.792 +0.000 -0.000 (20, 16, -3, 1) 95.9690 98.4292 +0.0040 -0.0014 74.9124 86.7262 -0.0121 -0.0049 99.144 99.792 -0.000 +0.000 (20, 16, -3, 0) 95.9358 98.4296 -0.0292 -0.0009 74.9443 86.7224 +0.0198 -0.0087 99.119 99.789 -0.025 -0.003 (21, 17, -3, -1) 95.7962 98.4268 -0.1689 -0.0038 74.9228 86.7618 -0.0016 +0.0307 98.887 99.756 -0.258 -0.036 (18, 14, -2, 1) 95.6803 98.3364 -0.2847 -0.0942 74.9116 86.6750 -0.0129 -0.0561 99.043 99.766 -0.102 -0.026 ``` ## Read length 100: Weighted SE/PE results - mapping-only ``` parameters acc_se acc_pe diff_se diff_pe mprt_se mprt_pe diff_se diff_pe (18, 14, 1, 3) 77.4674 86.7038 +0.6795 +0.4186 99.235 99.238 -0.367 -0.363 (17, 13, 1, 3) 77.4442 86.6853 +0.6563 +0.4001 99.266 99.267 -0.335 -0.335 (18, 14, 1, 2) 77.3444 86.6959 +0.5565 +0.4107 99.049 99.050 -0.552 -0.552 (16, 12, 1, 3) 77.3820 86.6520 +0.5941 +0.3668 99.289 99.288 -0.312 -0.314 (17, 13, 1, 2) 77.3103 86.6678 +0.5225 +0.3826 99.077 99.078 -0.524 -0.523 (16, 12, 1, 2) 77.2552 86.6521 +0.4673 +0.3669 99.092 99.090 -0.509 -0.511 (19, 15, 0, 3) 77.0658 86.4753 +0.2779 +0.1900 99.471 99.472 -0.131 -0.129 (18, 14, 0, 3) 77.0269 86.4572 +0.2390 +0.1720 99.484 99.484 -0.118 -0.118 (17, 13, 0, 3) 76.9784 86.4225 +0.1905 +0.1373 99.495 99.497 -0.107 -0.105 (20, 16, -2, 2) 76.7879 86.2852 +0.0000 +0.0000 99.601 99.602 +0.000 +0.000 ***** ``` ## Read length 100: Weighted SE/PE results - with extension alignment ``` parameters sacc_se sacc_pe diff_se diff_pe acc_se acc_pe diff_se diff_pe mprt_se mprt_pe diff_se diff_pe (18, 14, 1, 3) 96.9435 98.9435 +0.0754 +0.1069 80.2780 89.7660 +0.2204 +0.1587 99.235 99.773 -0.367 -0.033 (17, 13, 1, 3) 96.9600 98.9249 +0.0919 +0.0883 80.3083 89.7473 +0.2507 +0.1400 99.266 99.770 -0.335 -0.036 (16, 12, 1, 3) 96.9284 98.8981 +0.0604 +0.0615 80.2829 89.7221 +0.2254 +0.1148 99.289 99.770 -0.312 -0.036 (19, 15, 0, 3) 96.9144 98.8975 +0.0464 +0.0608 80.1322 89.6795 +0.0747 +0.0722 99.471 99.800 -0.131 -0.007 (18, 14, 1, 2) 96.7661 98.9275 -0.1019 +0.0909 80.2349 89.7641 +0.1774 +0.1568 99.049 99.744 -0.552 -0.063 (18, 14, 0, 3) 96.9002 98.8752 +0.0322 +0.0385 80.1610 89.6567 +0.1035 +0.0494 99.484 99.796 -0.118 -0.010 (17, 13, 1, 2) 96.7713 98.9019 -0.0968 +0.0653 80.2605 89.7290 +0.2030 +0.1217 99.077 99.743 -0.524 -0.064 (17, 13, 0, 3) 96.8696 98.8480 +0.0015 +0.0114 80.1623 89.6259 +0.1047 +0.0186 99.495 99.796 -0.107 -0.011 (16, 12, 1, 2) 96.7328 98.8816 -0.1352 +0.0449 80.2497 89.7367 +0.1921 +0.1295 99.092 99.739 -0.509 -0.067 (20, 16, -2, 2) 96.8680 98.8366 +0.0000 +0.0000 80.0575 89.6073 +0.0000 +0.0000 99.601 99.806 +0.000 +0.000 ***** ``` ## Read length 150: Weighted SE/PE results - mapping-only ``` parameters acc_se acc_pe diff_se diff_pe mprt_se mprt_pe diff_se diff_pe (21, 17, 2, 6) 83.8632 90.4686 +0.1062 +0.1215 99.734 99.734 -0.027 -0.028 (20, 16, 3, 6) 83.8398 90.4549 +0.0828 +0.1079 99.717 99.716 -0.045 -0.046 (20, 16, 2, 6) 83.8274 90.4234 +0.0703 +0.0763 99.740 99.740 -0.022 -0.021 (20, 16, 2, 7) 83.8496 90.4017 +0.0926 +0.0546 99.750 99.750 -0.012 -0.012 (20, 16, 1, 7) 83.7570 90.3470 +0.0000 +0.0000 99.762 99.762 -0.000 +0.000 ***** ``` ## Read length 150: Weighted SE/PE results - with extension alignment ``` parameters sacc_se sacc_pe diff_se diff_pe acc_se acc_pe diff_se diff_pe mprt_se mprt_pe diff_se diff_pe (21, 17, 2, 6) 98.0012 99.2737 +0.0169 +0.0303 86.2791 92.3460 +0.0071 +0.0317 99.734 99.781 -0.027 -0.000 (20, 16, 2, 7) 98.0302 99.2660 +0.0459 +0.0226 86.3007 92.3419 +0.0286 +0.0276 99.750 99.781 -0.012 -0.000 (20, 16, 3, 6) 97.9624 99.2791 -0.0219 +0.0357 86.2931 92.3486 +0.0210 +0.0344 99.717 99.780 -0.045 -0.001 (20, 16, 2, 6) 97.9862 99.2654 +0.0019 +0.0220 86.2931 92.3399 +0.0210 +0.0257 99.740 99.781 -0.022 -0.000 (20, 16, 1, 7) 97.9843 99.2434 +0.0000 +0.0000 86.2720 92.3143 +0.0000 +0.0000 99.762 99.781 -0.000 +0.000 ***** ``` ## Read length 200: Weighted SE/PE results - mapping-only ``` parameters acc_se acc_pe diff_se diff_pe mprt_se mprt_pe diff_se diff_pe (24, 20, 4, 10) 87.4239 91.8470 +0.0426 +0.0874 99.745 99.744 -0.005 -0.005 (23, 19, 4, 11) 87.4297 91.8294 +0.0484 +0.0697 99.747 99.745 -0.003 -0.003 (22, 18, 4, 13) 87.4156 91.7808 +0.0342 +0.0211 99.748 99.746 -0.002 -0.002 (22, 18, 2, 12) 87.3813 91.7597 +0.0000 +0.0000 99.750 99.748 +0.000 +0.000 ***** (20, 16, 4, 13) 87.3175 91.7053 -0.0638 -0.0543 99.749 99.748 -0.000 -0.000 ``` ## Read length 200: Weighted SE/PE results - with extension alignment ``` parameters sacc_se sacc_pe diff_se diff_pe acc_se acc_pe diff_se diff_pe mprt_se mprt_pe diff_se diff_pe (24, 20, 4, 10) 98.4480 99.3766 +0.0196 +0.0414 89.4568 93.1151 +0.0218 +0.0208 99.745 99.750 -0.005 +0.000 (23, 19, 4, 11) 98.4582 99.3671 +0.0298 +0.0319 89.4590 93.1004 +0.0240 +0.0061 99.747 99.750 -0.003 +0.000 (22, 18, 4, 13) 98.4712 99.3537 +0.0428 +0.0185 89.4698 93.1054 +0.0349 +0.0110 99.748 99.750 -0.002 +0.000 (22, 18, 4, 12) 98.4487 99.3562 +0.0203 +0.0211 89.4660 93.1114 +0.0310 +0.0170 99.748 99.750 -0.002 +0.000 (22, 18, 2, 12) 98.4284 99.3352 +0.0000 +0.0000 89.4350 93.0943 +0.0000 +0.0000 99.750 99.750 +0.000 +0.000 ***** (20, 16, 4, 13) 98.4127 99.3271 -0.0157 -0.0081 89.4412 93.0820 +0.0063 -0.0123 99.749 99.750 -0.000 +0.000 ``` ## Read length 300: Weighted SE/PE results - mapping-only ``` parameters acc_se acc_pe diff_se diff_pe mprt_se mprt_pe diff_se diff_pe (24, 20, 4, 12) 90.7514 94.5846 +0.1400 +0.0707 99.692 99.691 -0.000 -0.000 (23, 19, 5, 13) 90.7711 94.5733 +0.1598 +0.0593 99.692 99.691 +0.000 -0.000 (23, 19, 5, 12) 90.7296 94.5720 +0.1182 +0.0581 99.692 99.691 +0.000 -0.000 (22, 18, 7, 13) 90.7140 94.5651 +0.1027 +0.0511 99.692 99.691 -0.000 -0.000 (23, 19, 4, 12) 90.7349 94.5507 +0.1236 +0.0368 99.692 99.691 +0.000 +0.000 (23, 19, 3, 12) 90.7049 94.5552 +0.0936 +0.0413 99.692 99.691 +0.000 +0.000 (22, 18, 4, 13) 90.7233 94.5468 +0.1120 +0.0328 99.692 99.691 +0.000 +0.000 (22, 18, 4, 12) 90.6926 94.5512 +0.0813 +0.0373 99.692 99.691 +0.000 +0.000 (22, 18, 5, 12) 90.6904 94.5486 +0.0791 +0.0346 99.692 99.691 -0.000 -0.000 (22, 18, 7, 12) 90.6575 94.5556 +0.0462 +0.0417 99.692 99.691 -0.000 -0.000 (22, 18, 3, 13) 90.7065 94.5422 +0.0951 +0.0282 99.692 99.691 +0.000 +0.000 (22, 18, 4, 11) 90.6315 94.5504 +0.0202 +0.0365 99.692 99.691 -0.000 -0.000 (23, 19, 3, 11) 90.6476 94.5413 +0.0363 +0.0273 99.692 99.691 +0.000 +0.000 (22, 18, 3, 12) 90.6577 94.5379 +0.0464 +0.0240 99.692 99.691 +0.000 +0.000 (21, 17, 6, 13) 90.6749 94.5292 +0.0636 +0.0153 99.692 99.691 +0.000 -0.000 (23, 19, 2, 12) 90.6634 94.5319 +0.0521 +0.0179 99.692 99.691 +0.000 +0.000 (21, 17, 5, 12) 90.6420 94.5230 +0.0306 +0.0091 99.692 99.691 -0.000 -0.000 (22, 18, 2, 12) 90.6113 94.5139 +0.0000 +0.0000 99.692 99.691 +0.000 +0.000 ***** ``` ## Read length 300: Weighted SE/PE results - with extension alignment ``` parameters sacc_se sacc_pe diff_se diff_pe acc_se acc_pe diff_se diff_pe mprt_se mprt_pe diff_se diff_pe (24, 20, 4, 12) 98.7207 99.4493 +0.0601 +0.0175 92.4619 95.6001 +0.0303 +0.0337 99.692 99.691 -0.000 +0.000 (23, 19, 5, 13) 98.7216 99.4486 +0.0611 +0.0169 92.4686 95.5897 +0.0371 +0.0233 99.692 99.691 +0.000 -0.000 (23, 19, 5, 12) 98.7049 99.4498 +0.0443 +0.0181 92.4559 95.5806 +0.0244 +0.0142 99.692 99.691 +0.000 +0.000 (22, 18, 7, 13) 98.6930 99.4473 +0.0324 +0.0156 92.4516 95.5846 +0.0201 +0.0182 99.692 99.691 -0.000 +0.000 (23, 19, 4, 12) 98.7033 99.4423 +0.0427 +0.0105 92.4470 95.5845 +0.0155 +0.0181 99.692 99.691 +0.000 -0.000 (23, 19, 4, 11) 98.6870 99.4427 +0.0264 +0.0109 92.4326 95.5731 +0.0010 +0.0068 99.692 99.691 +0.000 +0.000 (22, 18, 4, 13) 98.6930 99.4399 +0.0325 +0.0081 92.4509 95.5854 +0.0193 +0.0191 99.692 99.691 +0.000 +0.000 (22, 18, 7, 12) 98.6703 99.4451 +0.0098 +0.0134 92.4344 95.5754 +0.0028 +0.0090 99.692 99.691 -0.000 +0.000 (22, 18, 5, 12) 98.6808 99.4406 +0.0203 +0.0088 92.4361 95.5781 +0.0046 +0.0117 99.692 99.691 -0.000 +0.000 (23, 19, 3, 12) 98.6826 99.4389 +0.0220 +0.0071 92.4384 95.5810 +0.0069 +0.0146 99.692 99.691 +0.000 -0.000 (22, 18, 3, 13) 98.6911 99.4366 +0.0305 +0.0049 92.4458 95.5765 +0.0143 +0.0101 99.692 99.691 +0.000 +0.000 (22, 18, 4, 12) 98.6791 99.4394 +0.0185 +0.0077 92.4351 95.5790 +0.0035 +0.0127 99.692 99.691 +0.000 +0.000 (22, 18, 3, 12) 98.6772 99.4363 +0.0166 +0.0046 92.4372 95.5819 +0.0056 +0.0155 99.692 99.691 +0.000 +0.000 (23, 19, 3, 11) 98.6741 99.4355 +0.0135 +0.0037 92.4297 95.5672 -0.0019 +0.0008 99.692 99.691 +0.000 +0.000 (21, 17, 6, 13) 98.6643 99.4370 +0.0037 +0.0052 92.4432 95.5756 +0.0117 +0.0092 99.692 99.691 +0.000 +0.000 (22, 18, 4, 11) 98.6591 99.4366 -0.0015 +0.0048 92.4134 95.5737 -0.0182 +0.0073 99.692 99.691 -0.000 +0.000 (23, 19, 2, 12) 98.6695 99.4322 +0.0089 +0.0005 92.4311 95.5719 -0.0004 +0.0055 99.692 99.691 +0.000 -0.000 (21, 17, 5, 12) 98.6512 99.4358 -0.0094 +0.0040 92.4250 95.5838 -0.0065 +0.0174 99.692 99.691 -0.000 +0.000 (22, 18, 2, 12) 98.6606 99.4318 +0.0000 +0.0000 92.4316 95.5664 +0.0000 +0.0000 99.692 99.691 +0.000 +0.000 ***** ``` ## Read length 500: Weighted SE/PE results - mapping-only ``` parameters acc_se acc_pe diff_se diff_pe mprt_se mprt_pe diff_se diff_pe (25, 19, 4, 13) 93.2463 95.3391 +0.1628 +0.0819 99.578 99.574 +0.000 +0.000 (25, 19, 5, 12) 93.2352 95.3397 +0.1518 +0.0825 99.578 99.574 +0.000 +0.000 (24, 18, 6, 13) 93.2172 95.3365 +0.1338 +0.0794 99.578 99.574 -0.000 -0.000 (24, 18, 5, 13) 93.2250 95.3340 +0.1416 +0.0768 99.578 99.574 +0.000 +0.000 (24, 18, 4, 13) 93.2231 95.3282 +0.1397 +0.0711 99.578 99.574 +0.000 +0.000 (25, 19, 3, 13) 93.2292 95.3211 +0.1457 +0.0639 99.578 99.574 +0.000 +0.000 (24, 18, 6, 12) 93.1847 95.3295 +0.1013 +0.0723 99.578 99.574 -0.000 -0.000 (25, 19, 3, 12) 93.1989 95.3234 +0.1155 +0.0662 99.578 99.574 +0.000 +0.000 (24, 18, 5, 12) 93.1781 95.3269 +0.0947 +0.0697 99.578 99.574 +0.000 +0.000 (24, 18, 6, 11) 93.1521 95.3260 +0.0686 +0.0688 99.578 99.574 -0.000 -0.000 (24, 18, 4, 12) 93.1863 95.3170 +0.1028 +0.0598 99.578 99.574 +0.000 +0.000 (24, 18, 5, 11) 93.1428 95.3261 +0.0593 +0.0689 99.578 99.574 +0.000 -0.000 (25, 19, 2, 13) 93.1886 95.3147 +0.1051 +0.0575 99.578 99.574 -0.000 -0.000 (24, 18, 3, 12) 93.1562 95.3096 +0.0728 +0.0525 99.578 99.574 +0.000 -0.000 (24, 18, 4, 11) 93.1424 95.3116 +0.0589 +0.0544 99.578 99.574 +0.000 +0.000 (23, 17, 5, 11) 93.1349 95.3104 +0.0514 +0.0532 99.578 99.574 +0.000 +0.000 (22, 16, 6, 13) 93.1627 95.2991 +0.0793 +0.0419 99.578 99.574 -0.000 -0.000 (23, 17, 4, 12) 93.1606 95.2940 +0.0772 +0.0368 99.578 99.574 +0.000 +0.000 (22, 16, 4, 13) 93.1598 95.2869 +0.0764 +0.0297 99.578 99.574 -0.000 +0.000 (23, 17, 6, 11) 93.1209 95.2940 +0.0375 +0.0368 99.578 99.574 +0.000 +0.000 (23, 17, 2, 12) 93.0834 95.2572 +0.0000 +0.0000 99.578 99.574 +0.000 +0.000 ***** ``` ## Read length 500: Weighted SE/PE results - with extension alignment ``` parameters sacc_se sacc_pe diff_se diff_pe acc_se acc_pe diff_se diff_pe mprt_se mprt_pe diff_se diff_pe (24, 18, 6, 13) 98.9471 99.3628 +0.0480 +0.0202 94.6823 96.0611 +0.0372 +0.0042 99.578 99.574 -0.000 +0.000 (24, 18, 5, 13) 98.9497 99.3618 +0.0505 +0.0192 94.6672 96.0698 +0.0220 +0.0130 99.578 99.574 +0.000 -0.000 (24, 18, 7, 13) 98.9453 99.3615 +0.0462 +0.0189 94.6771 96.0688 +0.0320 +0.0120 99.578 99.574 -0.000 +0.000 (24, 18, 5, 12) 98.9447 99.3609 +0.0455 +0.0183 94.6567 96.0654 +0.0116 +0.0086 99.578 99.574 +0.000 -0.000 (24, 18, 6, 12) 98.9406 99.3615 +0.0414 +0.0189 94.6616 96.0662 +0.0165 +0.0094 99.578 99.574 -0.000 +0.000 (24, 18, 5, 11) 98.9356 99.3618 +0.0365 +0.0192 94.6723 96.0657 +0.0272 +0.0088 99.578 99.574 +0.000 -0.000 (24, 18, 7, 12) 98.9345 99.3608 +0.0354 +0.0182 94.6654 96.0724 +0.0202 +0.0156 99.578 99.574 -0.000 +0.000 (25, 19, 5, 12) 98.9419 99.3588 +0.0427 +0.0162 94.6696 96.0604 +0.0244 +0.0036 99.578 99.574 +0.000 +0.000 (25, 19, 4, 13) 98.9430 99.3580 +0.0439 +0.0154 94.6639 96.0634 +0.0188 +0.0065 99.578 99.574 +0.000 +0.000 (24, 18, 6, 11) 98.9268 99.3601 +0.0277 +0.0175 94.6574 96.0676 +0.0123 +0.0108 99.578 99.574 -0.000 +0.000 (24, 18, 4, 11) 98.9328 99.3583 +0.0337 +0.0157 94.6595 96.0644 +0.0143 +0.0075 99.578 99.574 +0.000 -0.000 (24, 18, 4, 12) 98.9381 99.3566 +0.0389 +0.0140 94.6633 96.0668 +0.0182 +0.0099 99.578 99.574 +0.000 -0.000 (24, 18, 4, 13) 98.9441 99.3547 +0.0449 +0.0121 94.6718 96.0734 +0.0266 +0.0165 99.578 99.574 +0.000 -0.000 (24, 18, 5, 10) 98.9251 99.3591 +0.0260 +0.0165 94.6514 96.0552 +0.0063 -0.0017 99.578 99.574 +0.000 -0.000 (24, 18, 4, 10) 98.9219 99.3577 +0.0228 +0.0151 94.6460 96.0627 +0.0008 +0.0059 99.578 99.574 -0.000 -0.000 (23, 17, 5, 11) 98.9233 99.3559 +0.0241 +0.0133 94.6536 96.0629 +0.0085 +0.0061 99.578 99.574 +0.000 +0.000 (25, 19, 3, 12) 98.9333 99.3529 +0.0341 +0.0103 94.6648 96.0596 +0.0197 +0.0027 99.578 99.574 +0.000 -0.000 (24, 18, 6, 10) 98.9174 99.3567 +0.0183 +0.0141 94.6547 96.0626 +0.0096 +0.0058 99.578 99.574 -0.000 +0.000 (25, 19, 3, 13) 98.9323 99.3515 +0.0332 +0.0089 94.6630 96.0695 +0.0179 +0.0127 99.578 99.574 +0.000 -0.000 (24, 18, 3, 12) 98.9263 99.3506 +0.0272 +0.0080 94.6580 96.0602 +0.0129 +0.0034 99.578 99.574 +0.000 +0.000 (23, 17, 4, 12) 98.9211 99.3519 +0.0220 +0.0093 94.6395 96.0539 -0.0056 -0.0030 99.578 99.574 +0.000 +0.000 (23, 17, 6, 11) 98.9158 99.3531 +0.0166 +0.0104 94.6512 96.0580 +0.0061 +0.0011 99.578 99.574 +0.000 +0.000 (25, 19, 2, 13) 98.9266 99.3499 +0.0275 +0.0073 94.6582 96.0497 +0.0131 -0.0071 99.578 99.574 -0.000 -0.000 (22, 16, 4, 13) 98.9109 99.3416 +0.0117 -0.0010 94.6403 96.0507 -0.0048 -0.0062 99.578 99.574 -0.000 +0.000 (22, 16, 6, 13) 98.9088 99.3420 +0.0096 -0.0006 94.6504 96.0528 +0.0052 -0.0040 99.578 99.574 -0.000 +0.000 (23, 17, 2, 12) 98.8991 99.3426 +0.0000 +0.0000 94.6451 96.0568 +0.0000 +0.0000 99.578 99.574 +0.000 +0.000 ***** ```

[ksahlin]

I am unsure about read length 75 and 100: With these new settings, would decrease when going from read length 75 to 100, which is a bit unexpected.

Let's try with (19, 15, 0, 3).

Once @Itolstoganov PR is ready, let’s integrate these combinations and then I'll set off a larger benchmark.