| Row |
Paired-end read/Leif command |
File |
| 1 |
@SRR768303.40267220 HWI-ST1154:205:D1M9PACXX:7:2109:8467:24818 length=101
CTATTCCAAGTTATGCGGACACTATCGTCTGGATCGCTAAAGTGTGTCCACTGTCAGGCCGAACTGATTTCCAAACCAGCGCTGTGGTGGTCTGAGCGGAT
+SRR768303.40267220 HWI-ST1154:205:D1M9PACXX:7:2109:8467:24818 length=101
@@@DFDFDFHHDBBEBGHGIEHIEIIGEF?DHIIIIIGHIEI9B?@BBFF<88=CHCAC?HBD>B>@@@A3;-;@BD259?B@BDDC(2?@C@A@C@#### |
1.fastq.gz |
| 2 |
@SRR768303.40267220 HWI-ST1154:205:D1M9PACXX:7:2109:8467:24818 length=101
TTGTTCCCAGTCCGAACTGAACACCAGGGGCAGTAACGTTGTGGCCAGAACGCTGTACAGGATTCGATCGACAAAGCGATATTCCGCCTCACCCAGTTCGC
+SRR768303.40267220 HWI-ST1154:205:D1M9PACXX:7:2109:8467:24818 length=101
?@BB??DDHA??FGDHIIJJJGEH1CFFA<<FEF??BAHGGGGC=FHI;F=A4?EAC>ADE2;@CAA>;>@@@=?CABBB-&:@A(505<CA?ABB::@@@ |
2.fastq.gz |
| 3 |
leif fastq2fx step1.fx “#” SRR768303_1.fastq.gz SRR768303_2.fastq.gz human.fd |
|
| 4 |
@SRR768303.40267220 HWI-ST1154:205:D1M9PACXX:7:2109:8467:24818 length=101
CTATTCCAAGTTATGCGGACACTATCGTCTGGATCGCTAAAGTGTGTCCACTGTCAGGCCGAACTGATTTCCAAACCAGCGCTGTGGTGGTCTGAGCGGAT
TTGTTCCCAGTCCGAACTGAACACCAGGGGCAGTAACGTTGTGGCCAGAACGCTGTACAGGATTCGATCGACAAAGCGATATTCCGCCTCACCCAGTTCGC
+SRR768303.40267220 HWI-ST1154:205:D1M9PACXX:7:2109:8467:24818 length=101
@@@DFDFDFHHDBBEBGHGIEHIEIIGEF?DHIIIIIGHIEI9B?@BBFF<88=CHCAC?HBD>B>@@@A3;-;@BD259?B@BDDC(2?@C@A@C@!!!!
?@BB??DDHA??FGDHIIJJJGEH1CFFA<<FEF??BAHGGGGC=FHI;F=A4?EAC>ADE2;@CAA>;>@@@=?CABBB-&:@A(505<CA?ABB::@@@ |
step1.fx |
| 5 |
leif fxgroup step2.fx step1.fx |
|
| 6 |
@000001908_01_00@SRR768303_step1.fx@SRR768303.40267220 HWI-ST1154:205:D1M9PACXX:7:2109:8467:24818 length=101
CTATTCCAAGTTATGCGGACACTATCGTCTGGATCGCTAAAGTGTGTCCACTGTCAGGCCGAACTGATTTCCAAACCAGCGCTGTGGTGGTCTGAGCGGAT
TTGTTCCCAGTCCGAACTGAACACCAGGGGCAGTAACGTTGTGGCCAGAACGCTGTACAGGATTCGATCGACAAAGCGATATTCCGCCTCACCCAGTTCGC
+SRR768303.40267220 HWI-ST1154:205:D1M9PACXX:7:2109:8467:24818 length=101
@@@DFDFDFHHDBBEBGHGIEHIEIIGEF?DHIIIIIGHIEI9B?@BBFF<88=CHCAC?HBD>B>@@@A3;-;@BD259?B@BDDC(2?@C@A@C@!!!!
?@BB??DDHA??FGDHIIJJJGEH1CFFA<<FEF??BAHGGGGC=FHI;F=A4?EAC>ADE2;@CAA>;>@@@=?CABBB-&:@A(505<CA?ABB::@@@ |
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 1908 (read pair 0 of 1) ****
@000001908_00_01@SRR768303_step1.fx@SRR768303.40267220 HWI-ST1154:205:D1M9PACXX:7:2109:8467:24818 length=101
146148 -> 146248 "nt.fa.gz>gi|60279538|emb|BX927082.9| Zebrafish DNA sequence from clone DKEY-1"
Taxid[ 50%"Primates(9443)"]
Genus[ 52%"Danio(7954)" 50%"Microcebus(13149)"]
Species[ 52%"Danio rerio(7955)" 50%"Microcebus murinus(30608)"]
Consensus[ 52%"Danio rerio(7955)" 50%"Euteleostomi(117571)"]
gi_age[ 0% 0% 0% 0% 0% 0% 0% 52% 52% 52% 52% 52% 52% 52% 52% 52%]
CTATTCCAAGTTATGCGGACACTATCGTCTGGATCGCTAAAGTGTGTCCACTGTCAGGCCGAACTGATTTCCAAACCAGCGCTGTGGTGGTCTGAGCGGAT
|| | ||| | | ||| | || | || | || |||||||||||||||| | | |||| | | || | | | || | |
CTCCTAGAAGCAGTTTGAACAGAACTGTTTCAATAGGTATAGTGTGTCCACTGTCATATTGGAGTGATATAAACACTACAAGTCTTGTTTTTAAAATTTCA
44234 -> 44334 "wgs.fa.gz>gi|522805107|gb|ATTQ01000006.1| Rhizobium mongolense USDA 1844 A3C3"
Taxid[]
Genus[ 50%"Rhizobium(379)"]
Species[ 50%"Rhizobium mongolense(57676)"]
Consensus[ 50%"Rhizobium mongolense USDA 1844(1079460)"]
gi_age[ 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 0% 50%]
GCGAACTGGGTGAGGCGGAATATCGCTTTGTCGATCGAATCCTGTACAGCGTTCTGGCCACAACGTTACTGCCCCTGGTGTTCAGTTCGGACTGGGAACAA
|| || || || || | | | || | || | | | | | || ||||||||||||||||| | | |||||||
TCGTCTCGGTCGATGCCGATCTGCTGGCCCATAAGCCAACCAACCTCACCATGCGCGAGGCCGCGGCACTGCCCCTGGTGTTCATAACCGCCTGGGAAGGG
|
step3.qb |
| 11 |
leif qbmajority single 70 50 primate_ebv_phage.qb step4.qb step3.qb taxid.git Taxid 9443 10376 10841 |
|
| 12 |
[not output to this file] |
primate_ebv_phage.qb |
| 13 |
[unchanged, same as Row 10] |
step4.qb |
| 14 |
leif qbconsensus single 90 5 consensus.csv step4.qb taxid.git |
|
| 15 |
leif qbhistory histoty.csv step4.qb 0 50 60 70 80 90 |
|
| 16 |
leif qblowhom 90 below_90.fa step4.qb
leif qblowhom 90 below_90.fq step4.qb
leif qblowhom 90 below_90.qb step4.qb |
|
| 17 |
[unchanged, same as Row 10] |
below_90.qb |
| 18 |
>Group 1908, read 0
CTATTCCAAGTTATGCGGACACTATCGTCTGGATCGCTAAAGTGTGTCCACTGTCAGGCCGAACTGATTTCCAAACCAGCGCTGTGGTGGTCTGAGCGGAT
>Group 1908, read 1
GCGAACTGGGTGAGGCGGAATATCGCTTTGTCGATCGAATCCTGTACAGCGTTCTGGCCACAACGTTACTGCCCCTGGTGTTCAGTTCGGACTGGGAACAA |
below_90.fa |
| 19 |
blastn -query below_90.fa -remote -db "nt wgs refseq_genomic" -outfmt "7 stitle qcovs evalue pident" -dust no
-soft_masking no -task blastn |
|