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Published Histories | yinan | entire-pipeline-pe-hist
Import history

Galaxy History ' entire-pipeline-pe-hist'

DatasetAnnotation
1: HSV-McKr_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
2: HSV-McKr_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
3: JN555585_truncated.fasta
1 sequences
format: fasta, database: ?
Info:
uploaded fasta file
>JN555585_truncated
GTATATAAACCAACGAAAAGCGCGGGAACGGGGATACGGGGCTTGTGTGGCACGACGTCGTGGTTGTGTTACTGGGCAAACACTTGGGGACTGTAGGTTTCTGTGGGTGCCGACCCTAGGCGCTATGGGGATTTTGGGTTGGGTCGGGCTTATTGCCGTTGGGGTTTTGTGTGTGCGGGGGGGCTTGCCTTCAACCGAATATGTTATTCGGAGTCGGGTGGCTCGAGAGGTGGGGGATATATTAAAGGTGCCTTGT
GTGCCGCTCCCGTCTGACGATCTTGATTGGCGTTACGAGACCCCCTCGGCTATAAACTATGCTTTGATAGACGGTATATTTTTGCGTTATCACTGTCCCGGATTGGACACGGTCTTGTGGGATAGGCATGCCCAGAAGGCATATTGGGTTAACCCCTTTTTATTTGTGGCGGGTTTTTTGGAGGACTTGAGTTACCCCGCGTTTCCTGCCAACACCCAGGAAACAGAAACGCGCTTGGCCCTTTATAAAGAGATAC
GCCAGGCGCTGGACAGTCGCAAGCAGGCCGCCAGCCACACACCTGTGAAGGCTGGGTGTGTGAACTTTGACTATTCGCGCACCCGCCGCTGTGTAGGGCGACAGGATTTGGGACCTACCAACGGAACGTCTGGACGGACCCCGGTTCTGCCGCCGGACGATGAAGCGGGCCTGCAGCCGAAGCCCCTCACCACGCCGCCGCCCATCATCGCCACGTCGGACCCCACCCCGCGACGGGACGCCGCCACAAAAAGCAG
ACGCCGACGACCCCACTCCCGGCGCCTCTAACGATGCCTCGACGGAAACCCGTCCGGGTTCGGGGGGCGAACCGGCCGCCTGTCGCTCGTCAGGGCCGGCGGGCGCTCCTCGCCGCCCTAGAGGCTGTCCCGCTGGTGTGACGTTTTCCTCGTCCGCGCCCCCCGACCCTCCCATGGATTTAACAAACGGGGGGGTGTCGCCTGCGGCGACCTCGGCGCCTCTGGACTGGACCACGTTTCGGCGTGTGTTTCTGAT
CGACGACGCGTGGCGGCCCCTGATGGAGCCTGAGCTGGCGAACCCCTTAACCGCCCACCTCCTGGCCGAATATAATCGTCGGTGCCAGACCGAAGAGGTGCTGCCGCCGCGGGAGGATGTGTTTTCGTGGACTCGTTATTGCACCCCCGACGAGGTGCGCGTGGTTATCATCGGCCAGGACCCATATCACCACCCCGGCCAGGCGCACGGACTTGCGTTTAGCGTGCGCGCGAACGTGCCGCCTCCCCCGAGTCTT
4: assembled genome on data 1, data 3, and data 2.fasta
8 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 %
>scaffold1|size36562
CGCCCGCCCGCCCGCACACCATAACACCGAGAACAACACACGGGGGTGGGCGTAACATAATAAAGCTTTATTGGTAACTAGTTAACGGCAAGTCCGTGGGTGGCGCGACGGTGTCCTCCGGGCTCATCTCGTCGTCCTCGACGGGGGTGTTGGAATGAGGCGCCCCCTCGCGGTCCGCCTGGCGTGGGCCGTGCCCATAGGCCTCCGGCTTCTGTGCGTCCATGGGCATAGGCGCGGGGAGACTGTTTCCGGCGTC
GCGGACCTCCAGGTCCCTGGGAGACTCCGGTCCGGCTAACGGACGAAACGCGGAAGCGCGAAACACGCCGTCGGTGACCCGCAGGAGCTCGTTCATCAGTAACCAATCCATACTCAGCGTAACGGCCAGCCCCTGGCGAGACAGATCCACGGAGTCCGGAACCGCGGTCGTCTGGCCCAGGGGGCCGAGGCTGTAGTCCCCCCAGGCCCCTAGGTCGCGACGGCTCGTAAGCACGACGCGGTCGGCCGCGGGGCTT
TGCGGGGGGGCGTCCTCGGGCGCATGCGCCATTACCTCTCGGATGGCCGCGGCGCGCTGGTCGGCCGAGCTGACCAAGGGCGCCACGACCACGGCGCGCTCCGTCTGCAGGCCCTTCCACGTGTCGTGGAGTTCCTGGACAAACTCGGCCACGGGCTCGGGTCCCGCGGCCGCGCGCGCGGCTTGATAGCAGGCCGAGAGACGCCGCCAGCGCGCTAGAAACTGACCCATGAAGCAAAACCCGGGGACCTGGTCTC
CCGACAGCAGCTTCGACGCCCGGGTGTGAATGCCGGACACAACGGACAGAAACCCGTGAATTTCGCGCCGGACCACGGCCAGCACGTTGTCCTCGTGCGACACCTGGGCCGCCAGCTCGTCGCACACCCCCAGGTGCGCCGTGGTTTCGGTGATGACGGAACGCAGGCTCGCGAGGGACGCGACCAGCGCGCGCTTGGCGTCGTGATACATGCTGCAGTACTGACTCACCGCGTCCCCCATGGCCTCGGGGGGCCA
GGGCCCCAGGCGGTCGGGAGTGTCCCCGACCACCGCATACAGGCGGCGCCCGTCGCTCTCGAACCGACACTCGAAAAAGGCGGAGAGCGTGCGCATGTGCAGCCGCAGCAGCACGATGGCGTCCTCCAGTTGGCGAATCAGGGGGTCTGCGCGCTCGGCGAGGTCCTGCAGCACCCCCCGGGCGGCCAGGGCGTACATGCTAATCAACAGGAGGCTGGTGCCCACCTCGGGGGGCGGGGGGGGCTGCAGCTGGACC
5: Quast report on data 1, data 3, and data 2.html
2.0 KB
format: html, 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 %
HTML file
6: variation file on data 1, data 3, and data 2.vcf
734 lines, 2 comments
format: vcf, 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 %
1.Chrom2.Pos3.ID4.Ref5.Alt6.Qual7.Filter8.Info
##fileformat=VCFv4.1
#CHROMPOSIDREFALTQUALFILTERINFO
JN555585_truncated106nucmerG.0PASS.
JN555585_truncated145nucmerCT0PASS.
JN555585_truncated289nucmerTC0PASS.
JN555585_truncated449nucmerTC0PASS.
7: draft vs.reference comparison, result from data 1, data 3, and data 2.coords
14 lines
format: txt, 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 %
[R_St]	[R_Ed]	[T_St]	[T_Ed]	[% IDY]	[LEN_R]	[LEN_T]	[COV_R]	[COV_T]	[REF_ID]	[CGT_ID]
1	62450	47	62573	99.36	136376	71400	45.79	87.57	JN555585_truncated	scaffold2|size71400
53191	53334	53371	53228	100.00	136376	71400	0.11	0.20	JN555585_truncated	scaffold2|size71400
53191	53273	53455	53373	100.00	136376	71400	0.06	0.12	JN555585_truncated	scaffold2|size71400
62633	71434	62615	71400	99.22	136376	71400	6.45	12.31	JN555585_truncated	scaffold2|size71400
71435	108009	3	36562	99.54	136376	36562	26.82	99.99	JN555585_truncated	scaffold1|size36562
8: circos graph draft vs. reference on data 1, data 3, and data 2
48.3 KB
format: pdf, 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 %
Image in pdf format