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Table 1 Read recruitment results by using seed sets constructed with Bowtie2 and BWA

From: TAR-VIR: a pipeline for TARgeted VIRal strain reconstruction from metagenomic data

Bowtie2 Alignment
  Number Depth Coverage
   h1 h2 h3 h4 h5 h1 h2 h3 h4 h5
L,0,-0.3 55 0.13 0.01 0.06 0.15 0.12 0.01 0.01 0.01 0.01 0.01
L,0,-0.6 925 3.6 1.5 0.9 0.9 0.9 0.07 0.06 0.05 0.07 0.08
L,0,-0.9 8154 32 14 9 8 7 0.31 0.31 0.27 0.27 0.3
L,0,-1.2 13,221 49 24 15 13 10 0.43 0.45 0.42 0.44 0.43
  Recruitment
  Number Depth Coverage
   h1 h2 h3 h4 h5 h1 h2 h3 h4 h5
L,0,-0.3 45,504 182 89 59 41 11 1.0 1.0 1.0 1.0 0.37
L,0,-0.6 46,576 183 90 60 42 18 1.0 1.0 1.0 0.96 0.55
L,0,-0.9 52,337 198 96 63 46 37 1.0 1.0 1.0 0.98 0.99
L,0,-1.2 55,485 182 89 59 41 39 1.0 1.0 1.0 1.0 0.99
BWA Alignment
  Number Depth Coverage
   h1 h2 h3 h4 h5 h1 h2 h3 h4 h5
B:8 24,585 89 46 28 20 18 0.4 0.37 0.33 0.31 0.34
B:4 41,564 152 78 50 37 32 0.63 0.57 0.56 0.57 0.53
B:2 51,995 195 94 63 46 39 0.79 0.78 0.77 0.70 0.74
B:1 52,688 199 94 64 47 39 0.81 0.78 0.80 0.71 0.76
  Recruitment
  Number Depth Coverage
   h1 h2 h3 h4 h5 h1 h2 h3 h4 h5
B:8 62,609 235 117 75 55 44 1.0 1.0 1.0 1.0 0.99
B:4 72,901 270 135 89 65 53 1.0 1.0 1.0 1.0 1.0
B:2 79,755 299 146 97 71 58 1.0 1.0 1.0 1.0 1.0
B:1 78,540 294 143 96 70 57 1.0 1.0 1.0 1.0 1.0
  1. The “Alignment” section contains results for aligned reads. The “Recruitment” section contains results for recruited reads by TAR-VIR using the aligned reads. For each row, the aligned reads in “Alignment" section are the seed set for the recruited reads in “Recruitment” section. For Bowtie2, the “–score-min” parameter was set to allow different alignment error rates corresponding to 5%, 10%, 15%, and 20%, respectively. For BWA, “-A” is fixed as its default value 1. “-B” was modified to allow different error rate similar to Bowtie2. “Number” is the number of aligned or recruited reads. “Depth” is the average sequencing coverage. “Coverage” is the percentage of genome covering by at least one read. h1 to h5 represent the five SARS-CoV haplotypes
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