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Galaxy History ' workflow-pe-hist'

Dataset

Annotation

406: HSV-ls_read_1.fastq

3.9 GB
format: fastq, database: ?

Info: uploaded fastq file

@HWI-ST387:160:B07B8ABXX:5:1101:1617:1995 1:N:0:
NGGGTGGCACAGAACAGGGCCGAGAGAACGGGGGGCGGGTTGTTGGCCAGCAGGTACCGGGCCATGTACCAGTGGGGCCGGACGAACTCGTCGTCGAACGG
+
#4:D=A6D?CFHFHIFGGA;?F@FHI=GHHEABFB@BB@5?BBBBBCCCBBCBB@CCCBBB;7(9@ACDC:>>CC?@########################
@HWI-ST387:160:B07B8ABXX:5:1101:2362:1996 1:N:0:
NTAAGCGACAGAGGCAGTGTAGCGTAATGGCCTCGCGGTCGTAACTGGGGTATCGGCGCTGATATTTGACCACCAACGTGTACATGACGTTCCACAGGTCC

407: HSV-ls_read_3.fastq

3.9 GB
format: fastq, database: ?

Info: uploaded fastq file

@HWI-ST387:160:B07B8ABXX:5:1101:1617:1995 3:N:0:
TATCGCGGCTTCGCGGTGGCGGTCCTGACGGCCAACGAGGACCACGTGCACAGCCTGGCCGTGCCCCCCCTCGTTCTGCTGCACCGGTTCTCCCTGTTCAA
+
@@@BD;A@DFDBC>GHGGGFDGHAA@G=;=ED='6==5;',,9?A@9?8A@>(2<90<287<;02>?8;BBB@<288@CC@A?>>595<<3:A>9>>:4::
@HWI-ST387:160:B07B8ABXX:5:1101:2362:1996 3:N:0:
CGTTAGGCCACACCCTTTTGGAAGAGGCAATGAGCGGGGGGAAGGTTGGCCCGCACCGGCGCATGCAGGGTGCTGCACCAATCCGCGTGGAGTTGGGCCAT

408: JN555585_truncated.fasta

1 sequences
format: fasta, database: ?

Info:
uploaded fasta file

>JN555585_truncated
GTATATAAACCAACGAAAAGCGCGGGAACGGGGATACGGGGCTTGTGTGGCACGACGTCGTGGTTGTGTTACTGGGCAAACACTTGGGGACTGTAGGTTTCTGTGGGTGCCGACCCTAGGCGCTATGGGGATTTTGGGTTGGGTCGGGCTTATTGCCGTTGGGGTTTTGTGTGTGCGGGGGGGCTTGCCTTCAACCGAATATGTTATTCGGAGTCGGGTGGCTCGAGAGGTGGGGGATATATTAAAGGTGCCTTGT
GTGCCGCTCCCGTCTGACGATCTTGATTGGCGTTACGAGACCCCCTCGGCTATAAACTATGCTTTGATAGACGGTATATTTTTGCGTTATCACTGTCCCGGATTGGACACGGTCTTGTGGGATAGGCATGCCCAGAAGGCATATTGGGTTAACCCCTTTTTATTTGTGGCGGGTTTTTTGGAGGACTTGAGTTACCCCGCGTTTCCTGCCAACACCCAGGAAACAGAAACGCGCTTGGCCCTTTATAAAGAGATAC
GCCAGGCGCTGGACAGTCGCAAGCAGGCCGCCAGCCACACACCTGTGAAGGCTGGGTGTGTGAACTTTGACTATTCGCGCACCCGCCGCTGTGTAGGGCGACAGGATTTGGGACCTACCAACGGAACGTCTGGACGGACCCCGGTTCTGCCGCCGGACGATGAAGCGGGCCTGCAGCCGAAGCCCCTCACCACGCCGCCGCCCATCATCGCCACGTCGGACCCCACCCCGCGACGGGACGCCGCCACAAAAAGCAG
ACGCCGACGACCCCACTCCCGGCGCCTCTAACGATGCCTCGACGGAAACCCGTCCGGGTTCGGGGGGCGAACCGGCCGCCTGTCGCTCGTCAGGGCCGGCGGGCGCTCCTCGCCGCCCTAGAGGCTGTCCCGCTGGTGTGACGTTTTCCTCGTCCGCGCCCCCCGACCCTCCCATGGATTTAACAAACGGGGGGGTGTCGCCTGCGGCGACCTCGGCGCCTCTGGACTGGACCACGTTTCGGCGTGTGTTTCTGAT
CGACGACGCGTGGCGGCCCCTGATGGAGCCTGAGCTGGCGAACCCCTTAACCGCCCACCTCCTGGCCGAATATAATCGTCGGTGCCAGACCGAAGAGGTGCTGCCGCCGCGGGAGGATGTGTTTTCGTGGACTCGTTATTGCACCCCCGACGAGGTGCGCGTGGTTATCATCGGCCAGGACCCATATCACCACCCCGGCCAGGCGCACGGACTTGCGTTTAGCGTGCGCGCGAACGTGCCGCCTCCCCCGAGTCTT

409: Trim Sequence by Quality on data 406

3.6 GB
format: fastq, database: ?

@HWI-ST387:160:B07B8ABXX:5:1101:1617:1995 1:N:0:
GGGTGGCACAGAACAGGGCCGAGAGAACGGGGGGCGGGTTGTTGGCCAGCAGGTACCGGGCCATGTACCAGTGGGG
+
4:D=A6D?CFHFHIFGGA;?F@FHI=GHHEABFB@BB@5?BBBBBCCCBBCBB@CCCBBB;7(9@ACDC:>>CC?@
@HWI-ST387:160:B07B8ABXX:5:1101:2362:1996 1:N:0:
TAAGCGACAGAGGCAGTGTAGCGTAATGGCCTCGCGGTCGTAACTGGGGTATCGGCGCTGATATTTGACCACCAACGTGTACATGACGTTCCACAGGTCC

410: Trim Sequence by Quality on data 407

3.5 GB
format: fastq, database: ?

@HWI-ST387:160:B07B8ABXX:5:1101:1617:1995 3:N:0:
TATCGCGGCTTCGCGGTGGCGGTCCTGACGGCCAACGAGGACCACGTGCACAGCCTGGCCGTGCCCCCCCTCGTTCTGCTGCACCGGTTCTCCCTGTTCAA
+
@@@BD;A@DFDBC>GHGGGFDGHAA@G=;=ED='6==5;',,9?A@9?8A@>(2<90<287<;02>?8;BBB@<288@CC@A?>>595<<3:A>9>>:4::
@HWI-ST387:160:B07B8ABXX:5:1101:2362:1996 3:N:0:
CGTTAGGCCACACCCTTTTGGAAGAGGCAATGAGCGGGGGGAAGGTTGGCCCGCACCGGCGCATGCAGGGTGCTGCACCAATCCGCGTGGAGTTGGGCCAT

411: Merge Pair on data 410 and data 409

7.0 GB
format: fastq, database: ?

@HWI-ST387:160:B07B8ABXX:5:1101:1617:1995/1
GGGTGGCACAGAACAGGGCCGAGAGAACGGGGGGCGGGTTGTTGGCCAGCAGGTACCGGGCCATGTACCAGTGGGG
+
4:D=A6D?CFHFHIFGGA;?F@FHI=GHHEABFB@BB@5?BBBBBCCCBBCBB@CCCBBB;7(9@ACDC:>>CC?@
@HWI-ST387:160:B07B8ABXX:5:1101:1617:1995/2
TATCGCGGCTTCGCGGTGGCGGTCCTGACGGCCAACGAGGACCACGTGCACAGCCTGGCCGTGCCCCCCCTCGTTCTGCTGCACCGGTTCTCCCTGTTCAA

412: Reduce the coverage on data 411.se

314,389 sequences
format: fasta, database: ?

Info:
PARAMETERS:
- kmer size = 20 (-k)
- n hashes = 4 (-N)
- min hashsize = 1e+08 (-x)
- paired = True (-p)

Estimated memory usage is 4e+08 bytes (n_hashes x min_hashsize)
--------
making hashtable
... kept 122640 of 200000 , or 61 %

>HWI-ST387:160:B07B8ABXX:5:1101:5448:2054/1
TTATCAACTTATTTCTCTTTTCGATGGAATGTAGAT
>HWI-ST387:160:B07B8ABXX:5:1101:9099:2247/1
CAGGTTCAAGCAATTTTCCTGCCTCAGCCTCTCGAGTAGCTGGGACTACAGGCACACACCACCATGCCCTGCTAATTTTTGTATTTTTAGTAGAGACGAGG
>HWI-ST387:160:B07B8ABXX:5:1101:4354:1996/1
CACCACGGGGTTCACGTGAAACCCGGAAGTGGGGTCAAGGACCCTGGCCCCCTGGTACCCCACGTGCCGGCCGGCGGTCTCCCGCGCGCCCTCC

413: Reduce the coverage on data 411.pe

858,062 sequences
format: fasta, database: ?

>HWI-ST387:160:B07B8ABXX:5:1101:4498:2037/1
AGGGACCCCGCGTTGCCAGCCGCCGGGGTTCATCGGCACCCCGTGGTTACCCGGGGGTTGTCGGTGAAGGGTAGGGATTCATTCCCCAACCCCGGTCTCC
>HWI-ST387:160:B07B8ABXX:5:1101:4498:2037/2
GTCCAGGTGCCGGCCGCCGTGAAAGACGTACACGGACGAGCTGTAGTGCGATGGCGTCAGTTTCAGGGACACCGCGGTACCCCCGAGCCCCGTCGTGCGAG
>HWI-ST387:160:B07B8ABXX:5:1101:4265:2069/1
AATAAATAACACATAAATTTGGCTGGTTGTTTGTTGTCTTTAATGGACCGCCCGCAGGGGGGGTGGCATTTCA

414: Velvet on data 413 and data 412.fa

7,347 sequences
format: fasta, database: ?

Info:
[0.000001] Reading file '/mnt/galaxy/galaxy-dist/database/files/001/dataset_1229.dat' using 'Raw read' as FastA
[3.164147] 858062 sequences found
[3.164152] Done
[3.164218] Reading file '/mnt/galaxy/galaxy-dist/database/files/001/dataset_1228.dat' using

>contig1
CCGGCACGCCCCCAGGTAAAGTGTACATATACCAACCGCATATCAGACGCACCCGGCCCG
GAGCACCTGACCGTAAGCATCTGTGCCTCTCGCAGGGACCCCGCGTTGCCAGCCGCCGGG
GTTCATCGGCACCCCGTGGTTACCCGGGGGTTGTCGGTGAAGGGTAGGGATTCATTCCCC
AACCCCGGTCTCCCACCCTCCCCTTGACCGTCGCC
>contig2

415: draft genome on data 413, data 414, and data 408.fa

16 sequences
format: fasta, database: ?

>1
AGGGGAGAGGGGAGAGGGGGTATATAAACCAACGAAAAGCGCGGGAACGGGGATACGGGG
CTTGTGTGGCACGACGTCGTGGTTGTGTTACTGGGCAAACACTTGGGGACTGTAGGTTTC
TGTGGTGCCGACCCTAGGCGCTATGGGGATTTTGGGTTGGGTTGGGCTTATTGCCGTTGG
GGTTTTGTGTGTGCGGGGGGGCTTGCCTTCAACCGAATATGTTATTCGGAGTCGGGTGGC
TCGAGAGGTGGGGGATATATTAAAGGTGCCTTGTGTGCCGCTCCCGTCTGACGATCTTGA

416: scaffolded-genome after sspace on data 410, data 415, and data 409.fasta

4 sequences
format: fasta, database: ?

Info:
Your inserted inputs on [SSPACE_Basic_v2.0_linux] at Tue Sep 23 15:45:18 2014:
Required inputs:
-l = library.txt
-s = /mnt/galaxy/galaxy-dist/database/files/001/dataset_1231.dat
-b = sspace_out.tmp

Optional inputs:
-x = 1
-z = 0
-k = 5
-a = 0.7

>scaffold1|size117687
GGAGGGGGCGAGGGGCGGGAGGGGGCGAGGGGCGGTGGTGGTGCGCGGGCGCCCCCGGAGGGTTTGGATCTCTGACCTGAGATTGGCGGCACTGAGGTAGAGATGCCCGAACCCCCCCGAGGGAGCGCGGGACGCGGCTGGGGAGGGCTGGGGCTGGGGAGGGCTGGGGCTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCTGGGGAGGGCTGGGGCTGGGG
AGGGCTGGGGCTGTGGTGTGTGACAGGAGCGGCGTGTTGCGCTGGGGGACGTCTGGAGGAGCGGGGGGTGCGCGGTGACGTGTGGATGAGGAACAGGAGTTGTTGCGCGGTGAGTTGTCGCTGTGAGTTGTGTTGTTGGGCAGGTGTGGTGGATGACGTGACGTGTGGATGAGGAACCGGAGTCGCCGGTGCGCCGTGCTGTTGGTGTTCTGTTGGTGTTGTTACACCTGTGGCAGCCCGGGCCCCCCGCGCGCGG
GGCGGCGCGCAAAAAAGGCGGGCGGCGGTCCGGGCGGCGTGCGCGCGCGnGGAGCGGGGGAGGAGCCCCACCCACAGACGGGGAGGAGCGGGGGAGGAGCGGGGGAGGAGCGGGGGAGGAGCCCCACCCACAGACGGGGAGGAGCGGGGGAGGAGCGGCCAGACCCCAAAAACGGGCCCCCCCCGAAACACACCCCCCGGGGGTCGCGCGCGGCCCTTTAAAGCGCGGCGGCGGGCAGCCCGGGCCCCCCGCGGCC
GAGACTAGCGAGTTAGACAGGCAAGCACTACTCGCCTCTGCACGCACATGCTTGCCTGTCAAACTCTACCACCCCGGCACGCTCTCTGTCCCAACCGCCCAGNCCCAGGTAACCTCCACGCCCAACTCGGAACCCGCGGTCAGGAGCGCGCCCGCGGCCGCCCCGCCGCCGCCCCCCGCCGGTGGGCCCCCGCCTTCTTGTTCGCTGCTGCTGCGCCAGTGGCTCCACGTTCCCGAGTCCGCGTCCGACGACGACG
ATGACGACGACTGGCCGGACAGCCCCCCGCCCGAGCCGGCGCCAGAGGCCCGGCCCACCGCCGCCGCCCCCCGGCCCCGGTCCCCACCGCCCGGCGTGGGCCCGGGGGGCGGGGCTGACCCCTCCCACCCCCCCTCGCGCCCCTTCCGCCTTCCGCCGCGCCTCGCCCTCCGCCTGCGCGTCACCGCGGAGCACCTGGCGCGCCTGCGCCTGCGACGCGCGGGCGGGGAGGGGGCGCCGGAGCCCCCCGCGACCCC

417: quast_report on data 408 and data 416.html

2.0 KB
format: html, database: ?

Info:
/mnt/src/quast-2.2/quast.py -R /mnt/galaxy/galaxy-dist/database/files/000/dataset_35.dat -o /mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files /mnt/galaxy/galaxy-dist/database/files/001/dataset_1232.dat

Version 2.2, build

HTML file

418: snps on data 408 and data 416.vcf

814 lines, 2 comments
format: vcf, database: ?

1.Chrom 2.Pos 3.ID 4.Ref 5.Alt 6.Qual 7.Filter 8.Info
##fileformat=VCFv4.1
#CHROM POS ID REF ALT QUAL FILTER INFO
JN555585_truncated 106 nucmer G . 0 PASS .
JN555585_truncated 145 nucmer C T 0 PASS .
JN555585_truncated 289 nucmer T C 0 PASS .
JN555585_truncated 385 nucmer T C 0 PASS .

419: circos graph on data 408 and data 416

47.9 KB
format: pdf, database: ?

Info:
debuggroup summary 0.63s welcome to circos v0.64 2 May 2013
debuggroup summary 0.63s loading configuration from file output_circos.conf
debuggroup summary 0.63s found conf file output_circos.conf
debuggroup summary 1.93s debug will appear for these featu

Image in pdf format

420: Genome comparison on data 408 and data 416

14 lines
format: tabular, database: ?

1 2 3 4 5 6 7 8 9 10 11
[R_St] [R_Ed] [T_St] [T_Ed] [% IDY] [LEN_R] [LEN_T] [COV_R] [COV_T] [REF_ID] [CGT_ID]
1 62450 9788 72204 99.48 136376 117687 45.79 53.04 JN555585_truncated scaffold1|size117687
53191 53334 63086 62943 100.00 136376 117687 0.11 0.12 JN555585_truncated scaffold1|size117687
62633 108009 72246 117687 99.29 136376 117687 33.27 38.61 JN555585_truncated scaffold1|size117687
108111 108496 9610 9158 76.60 136376 117687 0.28 0.38 JN555585_truncated scaffold1|size117687
108497 113073 9043 4505 97.47 136376 117687 3.36 3.86 JN555585_truncated scaffold1|size117687

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Galaxy History ' workflow-pe-hist'

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