In [1]:
import pandas as pd
In [4]:
mock_community_df = pd.ExcelFile("../data/tables/mock-community-datasets.xlsx").parse('Sheet1', skiprows=1, index_col=0, index_row=0)
In [5]:
mock_community_df
Out[5]:
Target Gene
Region
Forward Primer
Reverse Primer
Sequencing Technology
Read Length (nt)
Paired End?
Composition
Number of Taxa
Sample Count / Type
Accession #*
Original Reference PMID
Download URL
Dataset Name
B1
16S
V4: F515-R806
GTGCCAGCMGCCGCGGTAA
GGACTACHVGGGTWTCTAAT
HiSeq
100
N
Mock Community A
48
1 even
1687
23202435
Forward part 1: https://s3.amazonaws.com/illum...
B2
16S
V4: F515-R806
GTGCCAGCMGCCGCGGTAA
GGACTACHVGGGTWTCTAAT
MiSeq
150
Y
Mock Community A
48
1 even
1688
23202435
Barcodes: https://s3.amazonaws.com/illumina-mo...
B3
16S
V4: F515-R806
GTGCCAGCMGCCGCGGTAA
GGACTACHVGGGTWTCTAAT
MiSeq
250
Y
Mock Community B
22
2 even 2 staggered
1685
23202435
Barcodes: https://s3.amazonaws.com/illumina-mo...
B4
16S
V4: F515-R806
GTGCCAGCMGCCGCGGTAA
GGACTACHVGGGTWTCTAAT
MiSeq
150
Y
Mock Community B
22
2 even 2 staggered
1686
23202435
Barcodes: https://s3.amazonaws.com/illumina-mo...
B5
16S
V4: F515-R806
GTGCCAGCMGCCGCGGTAA
GGACTACHVGGGTWTCTAAT
MiSeq
250
Y
Mock Community B
22
2 even 2 staggered
1972
23202435
Barcode: https://s3.amazonaws.com/illumina-moc...
B6
16S
V4: F515-R806
GTGCCAGCMGCCGCGGTAA
GGACTACHVGGGTWTCTAAT
GAIIx
100
Y
Mock Community C
67
3 even
719
20534432
Forward: https://s3.amazonaws.com/illumina-moc...
B7
16S
V4: F515-R806
GTGCCAGCMGCCGCGGTAA
GGACTACHVGGGTWTCTAAT
HiSeq
100
Y
Mock Community C
67
3 even
1319**
23332745
Forward: https://s3.amazonaws.com/illumina-moc...
B8
16S
V4: F515-R806
GTGCCAGCMGCCGCGGTAA
GGACTACHVGGGTWTCTAAT
HiSeq
100
Y
Mock Community C
67
3 even
1973
This Study
Forward: https://s3.amazonaws.com/illumina-moc...
F1
ITS
ITS1: ITS1-ITS4
CTTGGTCATTTAGAGGAAGTAA
GCTGCGTTCTTCATCGATGC
HiSeq
100
Y
Mock Community D
16
3 even
1974
This Study
Forward: https://s3.amazonaws.com/illumina-moc...
F2
ITS
ITS1: ITS1-ITS4
CTTGGTCATTTAGAGGAAGTAA
GCTGCGTTCTTCATCGATGC
HiSeq
100
Y
Mock Community D
16
3 even
1975
This Study
Forward part 1: https://s3.amazonaws.com/illum...
*Deposited in QIIME-db (microbio.me/qiime/) unless otherwise noted
NaN
NaN
NaN
NaN
NaN
NaN
NaN
NaN
NaN
NaN
NaN
NaN
NaN
**MG_RAST Project ID
NaN
NaN
NaN
NaN
NaN
NaN
NaN
NaN
NaN
NaN
NaN
NaN
NaN
Content source: nbokulich/short-read-tax-assignment
Similar notebooks: