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Pipeline.get_sample_names() fix for plate-replicates #108

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Pipeline.get_sample_names() fix for plate-replicates #108

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76a0244
Pipeline.get_sample_names() fix for plate-replicates
charles-cowart Oct 26, 2023
e72e79e
Update sequence_processing_pipeline/Pipeline.py
charles-cowart Oct 26, 2023
09422ae
Update sequence_processing_pipeline/Pipeline.py
charles-cowart Oct 26, 2023
a9a3d18
Update sequence_processing_pipeline/Pipeline.py
charles-cowart Oct 26, 2023
58522d0
Update sequence_processing_pipeline/Pipeline.py
charles-cowart Oct 26, 2023
acd7029
Updates based on feedback + additional test
charles-cowart Oct 26, 2023
c15568e
Added new test file
charles-cowart Oct 26, 2023
72cde70
restored removed lines from good-mapping-file.txt
charles-cowart Oct 27, 2023
593e469
Revamped _get_sample_names_from_mapping_file()
charles-cowart Oct 27, 2023
e033288
flake8
charles-cowart Oct 27, 2023
37338ba
Removed row-index from pre_prep_w_replicates.csv
charles-cowart Oct 27, 2023
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37 changes: 33 additions & 4 deletions sequence_processing_pipeline/Pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -459,21 +459,50 @@ def get_sample_names(self, project_name=None):

def _get_sample_names_from_sample_sheet(self, project_name):
if project_name is None:
return [x.Sample_Name for x in self.sample_sheet.samples]
if 'orig_name' in self.sample_sheet.samples[0]:
# return set as a list to match non-replicate results.
return sorted(list({x.orig_name for x in
self.sample_sheet.samples}))
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else:
return [x.Sample_Name for x in self.sample_sheet.samples]
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else:
# Since the project-name is stored in an internal variable
# in a third-party library, convert the data structure to
# JSON using the exposed method and obtain from the result.
jsn = json_loads(self.sample_sheet.to_json())
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return [x['Sample_Name'] for x in jsn['Data'] if
f'{project_name}_' in x['Sample_Project']]
if 'orig_name' in self.sample_sheet.samples[0]:
return [x['orig_name'] for x in jsn['Data']
if f'{project_name}_' in x['Sample_Project']]
else:
return [x['Sample_Name'] for x in jsn['Data']
if f'{project_name}_' in x['Sample_Project']]
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def _get_sample_names_from_mapping_file(self, project_name):
if project_name is None:
return list(self.mapping_file.sample_name)
if 'orig_name' in self.mapping_file.columns:
# because sample-names w/out replicate suffix will naturally
# appear more than once, we need to remove duplicates before
# returning them in list form. Sort the list to return a
# predictable order for testing.
return sorted(list(set(self.mapping_file.orig_name)))
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else:
return list(self.mapping_file.sample_name)
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else:
df = self.mapping_file[self.mapping_file['project_name'] ==
project_name]

# since orig_name is currently a required column whether or not
# the pre-prep file contains replicates, search for the presence
# of contains_replicates column instead, as it's not required for
# non-replicate pre-prep files.
if 'contains_replicates' in df.columns:
if set(df['contains_replicates']) == {True}:
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# contains_replicates should be either all True or all
# False. We need not assume non-boolean data-types.
# With replicates, assume there are duplicate entries in
# orig_name column.
return list(set((df['orig_name'])))

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return list(df['sample_name'])

def _parse_project_name(self, project_name, short_names):
Expand Down
8 changes: 3 additions & 5 deletions sequence_processing_pipeline/tests/data/good-mapping-file.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -162,17 +162,15 @@ Sample_Name BARCODE center_name center_project_name experiment_design_descriptio
6.22.22.RK.LH GTTGATACGATG UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4 GT 1331807 6.22.22.RK.LH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina LNH GTGTGYCAGCMGCCGCGGTAA 122822 1 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_238 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_238_6.22.22.RK.LH_E7 E7
6.22.22.RK.RH GAAGAGGGTTGA UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4 GT 1331807 6.22.22.RK.RH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina LNH GTGTGYCAGCMGCCGCGGTAA 122822 1 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_238 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_238_6.22.22.RK.RH_F7 F7
6.23.22.RK.FH AATGGTTCAGCA UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4 GT 1331807 6.23.22.RK.FH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina LNH GTGTGYCAGCMGCCGCGGTAA 122822 1 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_238 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_238_6.23.22.RK.FH_H8 H8
6.23.22.RK.LH.A TAACAATAATTC UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4 GT 1331807 6.23.22.RK.LH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina LNH GTGTGYCAGCMGCCGCGGTAA 122822 1 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_238 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_238_6.23.22.RK.LH_G8 G8
6.23.22.RK.LH.B GCTCGAAGATTC UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4 GT 1331807 6.23.22.RK.LH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina LNH GTGTGYCAGCMGCCGCGGTAA 122822 1 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_238 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_238_6.23.22.RK.LH_G10 G10
6.23.22.RK.LH TAACAATAATTC UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4 GT 1331807 6.23.22.RK.LH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina LNH GTGTGYCAGCMGCCGCGGTAA 122822 1 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_238 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_238_6.23.22.RK.LH_G8 G8
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6.24.22.RK.FH ACGACGCATTTG UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4 GT 1331807 6.24.22.RK.FH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina LNH GTGTGYCAGCMGCCGCGGTAA 122822 1 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_238 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_238_6.24.22.RK.FH_F10 F10
6.24.22.RK.RH ACTTGGTGTAAG UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4 GT 1331807 6.24.22.RK.RH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina LNH GTGTGYCAGCMGCCGCGGTAA 122822 1 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_238 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_238_6.24.22.RK.RH_E10 E10
6.25.22.RK.FH ACTACTGAGGAT UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4 GT 1331807 6.25.22.RK.FH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina LNH GTGTGYCAGCMGCCGCGGTAA 122822 1 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_238 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_238_6.25.22.RK.FH_A11 A11
6.25.22.RK.LH CACGTTTATTCC UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4 GT 1331807 6.25.22.RK.LH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina LNH GTGTGYCAGCMGCCGCGGTAA 122822 1 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_238 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_238_6.25.22.RK.LH_B11 B11
6.25.22.RK.RH CGCACCCATACA UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4 GT 1331807 6.25.22.RK.RH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina LNH GTGTGYCAGCMGCCGCGGTAA 122822 1 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_238 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_238_6.25.22.RK.RH_H10 H10
6.26.22.RK.FH CGGTGACCTACT UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4 GT 1331807 6.26.22.RK.FH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina LNH GTGTGYCAGCMGCCGCGGTAA 122822 1 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_238 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_238_6.26.22.RK.FH_C8 C8
6.26.22.RK.LH CTTAGTGCAGAA UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4 GT 1331807 6.26.22.RK.LH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina LNH GTGTGYCAGCMGCCGCGGTAA 122822 1 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_238 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_238_6.26.22.RK.LH_D8 D8
6.26.22.RK.RH.A GTCAACGCTGTC UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4 GT 1331807 6.26.22.RK.RH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina LNH GTGTGYCAGCMGCCGCGGTAA 122822 1 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_238 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_238_6.26.22.RK.RH_E8 E8
6.26.22.RK.RH.B TGAGTGGTCTGT UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4 GT 1331807 6.26.22.RK.RH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina LNH GTGTGYCAGCMGCCGCGGTAA 122822 1 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_238 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_238_6.26.22.RK.RH_F8 F8
6.26.22.RK.RH GTCAACGCTGTC UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4 GT 1331807 6.26.22.RK.RH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina LNH GTGTGYCAGCMGCCGCGGTAA 122822 1 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_238 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_238_6.26.22.RK.RH_E8 E8
6.27.22.RK.FH CATATAGCCCGA UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4 GT 1331807 6.27.22.RK.FH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina LNH GTGTGYCAGCMGCCGCGGTAA 122822 1 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_238 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_238_6.27.22.RK.FH_B8 B8
6.27.22.RK.LH TGAGTATGAGTA UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4 GT 1331807 6.27.22.RK.LH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina LNH GTGTGYCAGCMGCCGCGGTAA 122822 1 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_238 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_238_6.27.22.RK.LH_H7 H7
6.27.22.RK.RH AATTTAGGTAGG UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V4 GT 1331807 6.27.22.RK.RH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina LNH GTGTGYCAGCMGCCGCGGTAA 122822 1 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_238 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_238_6.27.22.RK.RH_A8 A8
Expand Down Expand Up @@ -240,7 +238,7 @@ Sample_Name BARCODE center_name center_project_name experiment_design_descriptio
9.2.22.RK.LH CTCCGAACAACA UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V168 GT 1331807 9.2.22.RK.LH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina MCM GTGTGYCAGCMGCCGCGGTAA 122822 4 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_242 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_242_9.2.22.RK.LH_A4 A4
9.2.22.RK.RH CCACTGCCCACC UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V180 GT 1331807 9.2.22.RK.RH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina MCM GTGTGYCAGCMGCCGCGGTAA 122822 4 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_242 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_242_9.2.22.RK.RH_B4 B4
9.20.22.RK.FH ACACCGCACAAT UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V151 GT 1331807 9.20.22.RK.FH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina MCM GTGTGYCAGCMGCCGCGGTAA 122822 3 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_240 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_240_9.20.22.RK.FH_G11 G11
9.20.22.RK.LH CAGCCCTACCCA UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V163 GT 1331807 9.20.22.RK,LH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina MCM GTGTGYCAGCMGCCGCGGTAA 122822 3 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_240 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_240_9.20.22.RK,LH_H11 H11
9.20.22.RK.LH CAGCCCTACCCA UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V163 GT 1331807 9.20.22.RK.LH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina MCM GTGTGYCAGCMGCCGCGGTAA 122822 3 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_240 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_240_9.20.22.RK,LH_H11 H11
9.20.22.RK.RH GTACTCGAACCA UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V139 GT 1331807 9.20.22.RK.RH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina MCM GTGTGYCAGCMGCCGCGGTAA 122822 3 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_240 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_240_9.20.22.RK.RH_F11 F11
9.21.22.RK.FH ATAGTCCTTTAA UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V136 GT 1331807 9.21.22.RK.FH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina MCM GTGTGYCAGCMGCCGCGGTAA 122822 3 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_240 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_240_9.21.22.RK.FH_F8 F8
9.21.22.RK.LH TATAGGCTCCGC UCSDMI Knight_ABTX Samples from ABTX NA NA Illumina MiSeq Illumina EMP protocol 515fbc, 806r amplification of 16S rRNA V160 GT 1331807 9.21.22.RK.LH FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT Illumina MCM GTGTGYCAGCMGCCGCGGTAA 122822 3 Echo 550 ABTX_20230208_ABTX_11052 14339 UCSDMI 2/7/23 ABTX_Plates_238_239_240_242_S1_L001 230207_M05314_0346_000000000-KVMGL ABTX_20230208_11052_Plate_240 Sequencing by synthesis 16S rRNA V4 108379Z NA NA 1317793 ABTX_20230208_11052_Plate_240_9.21.22.RK.LH_H8 H8
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