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Table 1

Example EBV paired-end read selected from SRR768303 (after each step of the workflow).

Row Paired-end read/Leif command File
1 @SRR768303.47548 HWI-ST1154:205:D1M9PACXX:7:1101:2354:9785 length=101

CGCTGCAAAGAGGCGAGGAATCTCCTTGTAATGGACATCCTCCTTCTTGGCCCCCAGTAGGTGCCTGGCTACTGTGTCCAGCTTGTAGTCTGAGAGGCTGA

+SRR768303.47548 HWI-ST1154:205:D1M9PACXX:7:1101:2354:9785 length=101

@BCFFFFFHHHHGAFFHJEIIJJJJJIJGGIJJJIJIJIIIGIIIFIIHIICGIHHFDFFFFECEEDDBDDDDDEACDDDDDCDDBDDDDCCCDCDDBDD?
1.fastq.gz
2 @SRR768303.47548 HWI-ST1154:205:D1M9PACXX:7:1101:2354:9785 length=101
CGGGCAAGGGCTTCTTGCGGGCCAACACCAAGGTCCGCATCACCGGCCTCATCCCCATCGACATGTACGCCGTGTGCCGGGACAAGCTCAGCCTCTCAGAC
+SRR768303.47548 HWI-ST1154:205:D1M9PACXX:7:1101:2354:9785 length=101
CCCFFFFFHHGHHJIIIIJJJDFHJIGJJJJJIHIJJJJJFHGHEFCDDDCCDDDDDDDDD@BBDDEED&5>>BB?CDDDD@DDB@?CDDDDDDDCCCDDD
 2.fastq.gz
3 leif fastq2fx step1.fx “#” SRR768303_1.fastq.gz SRR768303_2.fastq.gz human.fd ebv.fd phage.fd
4 @SRR768303.47548 HWI-ST1154:205:D1M9PACXX:7:1101:2354:9785 length=101
CGCTGCAAAGAGGCGAGGAATCTCCTTGTAATGGACATCCTCCTTCTTGGCCCCCAGTAGGTGCCTGGCTACTGTGTCCAGCTTGTAGTCTGAGAGGCTGA
CGGGCAAGGGCTTCTTGCGGGCCAACACCAAGGTCCGCATCACCGGCCTCATCCCCATCGACATGTACGCCGTGTGCCGGGACAAGCTCAGCCTCTCAGAC
+SRR768303.47548 HWI-ST1154:205:D1M9PACXX:7:1101:2354:9785 length=101
@BCFFFFFHHHHGAFFHJEIIJJJJJIJGGIJJJIJIJIIIGIIIFIIHIICGIHHFDFFFFECEEDDBDDDDDEACDDDDDCDDBDDDDCCCDCDDBDD?
CCCFFFFFHHGHHJIIIIJJJDFHJIGJJJJJIHIJJJJJFHGHEFCDDDCCDDDDDDDDD@BBDDEED&5>>BB?CDDDD@DDB@?CDDDDDDDCCCDDD
step1.fx
5 leif fxgroup step2.fx step1.fx
6 @000000011_3546_02@step1.fx@SRR768303.47548 HWI-ST1154:205:D1M9PACXX:7:1101:2354:9785 length=101
CGCTGCAAAGAGGCGAGGAATCTCCTTGTAATGGACATCCTCCTTCTTGGCCCCCAGTAGGTGCCTGGCTACTGTGTCCAGCTTGTAGTCTGAGAGGCTGA
CGGGCAAGGGCTTCTTGCGGGCCAACACCAAGGTCCGCATCACCGGCCTCATCCCCATCGACATGTACGCCGTGTGCCGGGACAAGCTCAGCCTCTCAGAC
+SRR768303.47548 HWI-ST1154:205:D1M9PACXX:7:1101:2354:9785 length=101
@BCFFFFFHHHHGAFFHJEIIJJJJJIJGGIJJJIJIJIIIGIIIFIIHIICGIHHFDFFFFECEEDDBDDDDDEACDDDDDCDDBDDDDCCCDCDDBDD?
CCCFFFFFHHGHHJIIIIJJJDFHJIGJJJJJIHIJJJJJFHGHEFCDDDCCDDDDDDDDD@BBDDEED&5>>BB?CDDDD@DDB@?CDDDDDDDCCCDDD
step2.fx
7 leif fxsample 0 1 step3.fx step2.fx  
8 [unchanged, same as Row 6] step3.fx
9 leif qblast qblast_settings.txt taxid.git blast_*.fa.gz step3.fx  
10 **** Group 11 (read pair 2 of 3546) ****
@000000011_02_3546@step1.fx@SRR768303.47548 HWI-ST1154:205:D1M9PACXX:7:1101:2354:9785 length=101

167132 -> 167319 "nt.fa.gz>gi|330330|gb|M80517.1|HS4B958RAJ Epstein-Barr virus, artifactual joi" 
Taxid[  99%"Human herpesvirus 4(10376)"]
Genus[  99%"Lymphocryptovirus(10375)"]
Species[  99%"Human herpesvirus 4(10376)"  91%"Pan troglodytes lymphocryptovirus 1(212727)" ]
Consensus[  99%"Human herpesvirus 4(10376)"  91%"Lymphocryptovirus(10375)"]
gi_age[  99%  99%  99%  99%  99%  99%  99%  99%  99%  99%  99%  99%  99%  99%  99%  99%]
@BCFFFFFHHHHGAFFHJEIIJJJJJIJGGIJJJIJIJIIIGIIIFIIHIICGIHHFDFFFFECEEDDBDDDDDEACDDDDDCDDBDDDDCCCDCDDBDD?
CGCTGCAAAGAGGCGAGGAATCTCCTTGTAATGGACATCCTCCTTCTTGGCCCCCAGTAGGTGCCTGGCTACTGTGTCCAGCTTGTAGTCTGAGAGGCTGA ------->
||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CGCTGCAAAGAGGCGAGGAATCTCCTTGTAATGCACATCCTCCTTCTTGGCCCCCAGTAGGTGCCTGGCTACTGTGTCCAGCTTGTAGTCTGAGAGGCTGA - -14 ->

DDDCCCDDDDDDDC?@BDD@DDDDC?BB>>5&DEEDDBB@DDDDDDDDDCCDDDCFEHGHFJJJJJIHIJJJJJGIJHFDJJJIIIIJHHGHHFFFFFCCC
GTCTGAGAGGCTGAGCTTGTCCCGGCACACGGCGTACATGTCGATGGGGATGAGGCCGGTGATGCGGACCTTGGTGTTGGCCCGCAAGAAGCCCTTGCCCG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GTCTGAGAGGCTGAGCTTGTCCCGGCACACGGCGTACATGTCGATGGGGATGAGGCCGGTGATGCGGACCTTGGTGTTGGCCCGCAAGAAGCCCTTGCCCG

step3.qb
11 leif qbmajority single 70 50 primate_ebv_phage.qb step4.qb step3.qb taxid.git Taxid 9443 10376 10841  
12 [unchanged, same as Row 10] primate_ebv_phage.qb

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