Leif™‎ > ‎Workflow and Tutorial‎ > ‎

Table 2

Example candidate novel microorganism paired-end read selected from SRR768303 (after each step of the workflow):

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


Comments