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 |
|
|