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Ivarz / Conifer

Calculate confidence scores from Kraken2 output
BSD 2-Clause "Simplified" License
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length and confidence length differ #10

Open TomhitsJerry opened 1 year ago

TomhitsJerry commented 1 year ago

Hi, Ivarz: Thanks for your convenient tool. I am trying to calculate confidence score using result from kraken2. I am wondering why len not equal to 100?

C V100006960L1C001R001000420 853 100|100 0：16 853：8 1783272：2 748224：2 1783272：2 168384：5 186801：6 0：2 168384：5 0：18 |：|748224:7 0:2 748224:5 0:21 853:4 748224:7 0:5 748224:3 0:12 read1 : 16+8+2+2+2+5+6+2+5+18=66, read2: 7+2+5+21+4+7+5+3+12=66. Thanks!

Ivarz commented 1 year ago

Hi TomhitsJerry!

In this case 100 is paired-end read length (in base pairs) and the next column represents classification of every k-mer in the paired-end read. By default Kraken2's k-mer length is 35 bp and the total number of k-mers in a read is 100-35+1 = 66.