README
¶
Evaluation
Number of matched strobemers
A similar test with approximate results.
query: 150bp, snp: 1 (0.006)
$ go run test1_matches.go q0-snp1.fasta r0.fasta | csvtk pretty -t
query ref method nQuery nRef nCommon qCov
------- --- ------------------------------ ------ ------- ------- -----
q0-snp1 r0 Kmer(20) 131 1546586 111 84.73 *
q0-snp1 r0 MinStrobes(2,10,12,12,shrink) 131 1548767 109 83.21
q0-snp1 r0 MinStrobes(2,10,12,12) 129 1548765 109 84.50
q0-snp1 r0 RankStrobes(2,10,12,12,shrink) 131 1548767 109 83.21
q0-snp1 r0 RankStrobes(2,10,12,12) 129 1548765 109 84.50
q0-snp1 r0 Kmer(21) 130 1547218 109 83.85
q0-snp1 r0 MinStrobes(3,7,9,9,shrink) 126 1549315 108 85.71 *
q0-snp1 r0 MinStrobes(3,7,9,9) 126 1549315 108 85.71 *
q0-snp1 r0 RankStrobes(3,7,9,9,shrink) 126 1549315 108 85.71 *
q0-snp1 r0 RankStrobes(3,7,9,9) 126 1549315 108 85.71 *
q0-snp1 r0 Kmer(20) 131 1546586 111 84.73
q0-snp1 r0 MinStrobes(2,10,12,16,shrink) 131 1548376 107 81.68
q0-snp1 r0 MinStrobes(2,10,12,16) 125 1548370 107 85.60 *
q0-snp1 r0 RankStrobes(2,10,12,16,shrink) 131 1548438 108 82.44
q0-snp1 r0 RankStrobes(2,10,12,16) 125 1548432 108 86.40 *
q0-snp1 r0 Kmer(21) 130 1547218 109 83.85
q0-snp1 r0 MinStrobes(3,7,9,13,shrink) 122 1545403 102 83.61
q0-snp1 r0 MinStrobes(3,7,9,13) 118 1545399 102 86.44 **
q0-snp1 r0 RankStrobes(3,7,9,13,shrink) 122 1545522 107 87.70 **
q0-snp1 r0 RankStrobes(3,7,9,13) 118 1545518 105 88.98 **
query: 150bp, snp: 3 (0.02)
$ go run test1_matches.go q2-snp3.fasta r2.fasta | csvtk pretty -t
query ref method nQuery nRef nCommon qCov
------- --- ------------------------------ ------ ------- ------- -----
q2-snp3 r2 Kmer(20) 131 1687558 84 64.12 *
q2-snp3 r2 MinStrobes(2,10,12,12,shrink) 131 1687785 82 62.60
q2-snp3 r2 MinStrobes(2,10,12,12) 129 1687783 82 63.57
q2-snp3 r2 RankStrobes(2,10,12,12,shrink) 131 1687785 82 62.60
q2-snp3 r2 RankStrobes(2,10,12,12) 129 1687783 82 63.57
q2-snp3 r2 Kmer(21) 130 1687656 82 63.08
q2-snp3 r2 MinStrobes(3,7,9,9,shrink) 126 1687865 84 66.67 *
q2-snp3 r2 MinStrobes(3,7,9,9) 126 1687865 84 66.67 *
q2-snp3 r2 RankStrobes(3,7,9,9,shrink) 126 1687865 84 66.67 *
q2-snp3 r2 RankStrobes(3,7,9,9) 126 1687865 84 66.67 *
q2-snp3 r2 Kmer(20) 131 1687558 84 64.12 *
q2-snp3 r2 MinStrobes(2,10,12,16,shrink) 131 1687487 76 58.02
q2-snp3 r2 MinStrobes(2,10,12,16) 125 1687481 76 60.80
q2-snp3 r2 RankStrobes(2,10,12,16,shrink) 131 1687529 77 58.78
q2-snp3 r2 RankStrobes(2,10,12,16) 125 1687523 76 60.80
q2-snp3 r2 Kmer(21) 130 1687656 82 63.08 *
q2-snp3 r2 MinStrobes(3,7,9,13,shrink) 122 1684611 74 60.66
q2-snp3 r2 MinStrobes(3,7,9,13) 118 1684607 72 61.02
q2-snp3 r2 RankStrobes(3,7,9,13,shrink) 122 1684661 71 58.20
q2-snp3 r2 RankStrobes(3,7,9,13) 118 1684657 68 57.63
query: 150bp, snp: 7 (0.47)
$ go run test1_matches.go q1-snp7.rc.fasta r1.fasta | csvtk pretty -t
query ref method nQuery nRef nCommon qCov
---------- --- ------------------------------ ------ ------- ------- -----
q1-snp7.rc r1 Kmer(20) 131 2802879 54 41.22 *
q1-snp7.rc r1 MinStrobes(2,10,12,12,shrink) 131 2804781 52 39.69
q1-snp7.rc r1 MinStrobes(2,10,12,12) 129 2804779 52 40.31
q1-snp7.rc r1 RankStrobes(2,10,12,12,shrink) 131 2804781 52 39.69
q1-snp7.rc r1 RankStrobes(2,10,12,12) 129 2804779 52 40.31
q1-snp7.rc r1 Kmer(21) 130 2804365 51 39.23 *
q1-snp7.rc r1 MinStrobes(3,7,9,9,shrink) 126 2806161 48 38.10
q1-snp7.rc r1 MinStrobes(3,7,9,9) 126 2806161 48 38.10
q1-snp7.rc r1 RankStrobes(3,7,9,9,shrink) 126 2806161 48 38.10
q1-snp7.rc r1 RankStrobes(3,7,9,9) 126 2806161 48 38.10
q1-snp7.rc r1 Kmer(20) 131 2802879 54 41.22 *
q1-snp7.rc r1 MinStrobes(2,10,12,16,shrink) 131 2803507 51 38.93
q1-snp7.rc r1 MinStrobes(2,10,12,16) 125 2803501 51 40.80
q1-snp7.rc r1 RankStrobes(2,10,12,16,shrink) 131 2803659 47 35.88
q1-snp7.rc r1 RankStrobes(2,10,12,16) 125 2803653 44 35.20
q1-snp7.rc r1 Kmer(21) 130 2804365 51 39.23 *
q1-snp7.rc r1 MinStrobes(3,7,9,13,shrink) 122 2797218 36 29.51
q1-snp7.rc r1 MinStrobes(3,7,9,13) 118 2797214 36 30.51
q1-snp7.rc r1 RankStrobes(3,7,9,13,shrink) 122 2797918 42 34.43
q1-snp7.rc r1 RankStrobes(3,7,9,13) 118 2797914 41 34.75
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