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Sequencing summary

The sequencing summary is a TSV file, containing one row per read. It is intended to allow fast analysis of the results of a sequencing run.

Columns

filename_fastq

Regex [A-Za-z0-9\-_\.]+
Required
Only When online
Examples
PBC012345_pass_unclassified_2abce119_646d7417_0.fastq.gz
PBC012345_fail_2abce119_646d7417_0.fastq.gz

The name of the FASTQ file that contains this read.

filename_fast5

Regex [A-Za-z0-9\-_\.]+
Required
Only When online
Examples
PBC012345_pass_unclassified_2abce119_646d7417_0.fast5
PBC012345_fail_unclassified_2abce119_646d7417_0.fast5
PBC012345_fail_2abce119_646d7417_0.fast5

The name of the fast5 file that contains this read.

filename_pod5

Regex [A-Za-z0-9\-_\.]+
Required
Only When online
Examples
PBC012345_pass_unclassified_2abce119_646d7417_0.pod5
PBC012345_fail_2abce119_646d7417_0.pod5

The name of the POD5 file that contains this read.

filename_bam

Regex [A-Za-z0-9\-_\.]+
Required
Only When online
Examples
PBC012345_pass_unclassified_2abce119_646d7417_0.bam
PBC012345_fail_2abce119_646d7417_0.bam

The name of the BAM file that contains this read.

input_filename

Regex [A-Za-z0-9\-_\.]+
Required
Only When offline
Examples
PBC012345_pass_unclassified_2abce119_646d7417_0.pod5
PBC012345_fail_2abce119_646d7417_0.fast5

The name of the input .fast5 or POD5 file.

batch_id

Regex [0-9]+
Required
Only When offline
Examples
1
512
3000

Identifies the batch of reads to which this read belongs.

parent_read_id

Regex [a-f0-9]{8}-[a-f0-9]{4}-[4-5][a-f0-9]{3}-[89ab][a-f0-9]{3}-[a-f0-9]{12}
Required
Common fields FASTQ: parent_read_idBAM: pi
Examples
e4994c62-93f9-439a-bc8f-d20c95a137a5

The read_id of the read which was the source of this entry. This may be the same as the read id if no read splitting was performed for this read, or will be a new globally unique UUID value if this read was split out of another read by the basecaller.

read_id

Regex [a-f0-9]{8}-[a-f0-9]{4}-[4-5][a-f0-9]{3}-[89ab][a-f0-9]{3}-[a-f0-9]{12}
Required
Examples
e4994c62-93f9-439a-bc8f-d20c95a137a5

A unique UUID for the sequenced read.

run_id

Regex [a-f0-9]{8}-[a-f0-9]{4}-[4-5][a-f0-9]{3}-[89ab][a-f0-9]{3}-[a-f0-9]{12}
Required
Common fields FASTQ: runidBAM: DS
Examples
e4994c62-93f9-439a-bc8f-d20c95a137a5

The unique run identifier for the sequencing run.

channel

Regex [0-9]+
Required
Common fields FASTQ: chBAM: ch
Examples
1
512
3000

The 1 indexed number for the channel the read was sequenced on.

mux

Regex 1|2|3|4
Required
Examples
1

The 1 indexed number for the mux the read was sequenced on.

minknow_events

Regex [0-9]+
Required
Examples
4323

The number of events detected by MinKNOW for this read.

start_time

Regex [0-9]+\.[0-9]+
Required
Common fields FASTQ: start_timeBAM: st
Examples
10.4

The time the read started in seconds from the start of the run.

duration

Regex [0-9]+\.[0-9]+
Required
Examples
5.4

The duration of the read in seconds.

passes_filtering

Regex TRUE|FALSE
Required
Only When basecalling
Examples
TRUE
FALSE

Whether the read passed any filtering steps performed.

template_start

Regex [0-9]+\.[0-9]+
Required
Only When basecalling
Examples
10.7

The start time of the template read in seconds from the start of the run.

num_events_template

Regex [0-9]+
Required
Only When basecalling
Examples
1000

The number of events detected by the basecaller for the template read.

template_duration

Regex [0-9]+\.[0-9]+
Required
Only When basecalling
Examples
100.3

The duration of the template read in seconds.

sequence_length_template

Regex [0-9]+
Required
Only When basecalling
Examples
6734

The length of the template read in bases.

mean_qscore_template

Regex [0-9]+\.[0-9]+
Required
Only When basecalling
Examples
20.4

The mean qscore of the template read.

poly_tail_length

Regex -1|[0-9]+
Required
Only When poly_a_tail_estimation
Examples
-1
100

The length of the poly-A tail detected in the read.

poly_tail_start

Regex -1|[0-9]+
Required
Only When poly_a_tail_estimation
Examples
-1
100

The start sample of the poly-A tail detected in the read.

poly_tail_end

Regex -1|[0-9]+
Required
Only When poly_a_tail_estimation
Examples
-1
100

The end sample of the poly-A tail detected in the read.

poly_tail2_start

Regex -1|[0-9]+
Required
Only When poly_a_tail_estimation
Examples
-1
100

The start sample of the split poly-A tail detected in the read.

poly_tail2_end

Regex -1|[0-9]+
Required
Only When poly_a_tail_estimation
Examples
-1
100

The end sample of the split poly-A tail detected in the read.

pore_type

Regex [a-zA-Z0-9_\.]+
Required
Examples
r9.4.1
r10.4.1
not_set

The type of the pore in use for this read.

experiment_id

Regex [A-Za-z0-9\-_\.]+
Required
Examples
My_Group
my-group-1

The user specified identifier for the group of sequencing runs.

sample_id

Regex [A-Za-z0-9\-_\.]+
Required
Common fields FASTQ: sample_idBAM: LBSample sheet: sample_id
Examples
My_Sample
my-sample-1

The user specified identifier for the sequencing run.

end_reason

Regex unknown|signal_positive|signal_negative|mux_change|unblock_mux_change|data_service_unblock_mux_change|analysis_config_change|device_data_error|api_request|paused
Required
Examples
signal_positive
signal_negative

The reason the read ended.

alias

Regex unclassified|[A-Za-z0-9\-_\.]+
Required
Only When barcoding
Common fields FASTQ: barcode_aliasBAM: alSample sheet: alias
Examples
unclassified
my_sample
sample01

The user-supplied alias for the barcode.

type

Regex na|test_sample|positive_control|negative_control|no_template_control|positive_control_1|positive_control_2
Required
Only When barcoding
Examples
test_sample
positive_control

The type of the data the read's associated barcode is related to.

barcode_arrangement

Regex -|unclassified|[A-Za-z0-9\-_\.]+
Required
Only When barcoding
Common fields FASTQ: barcodeBAM: SMSample sheet: barcode
Examples
-
barcode01
unclassified

The barcode identified for the read. If barcoding was not performed for the read a value of - is used.

barcode_kit

Regex -|[A-Za-z0-9\-_\.]+
Required
Only When barcoding
Examples
-
SQK-NDB114-96

The kit used for barcoding. If barcoding was not performed for the read a value of - is used.

barcode_variant

Regex -|n/a|var1|var2
Required
Only When barcoding
Examples
-
n/a
var1
var2

The arrangement variant of the found barcode. If barcoding was not performed for the read a value of - is used.

barcode_score

Regex -|-?[0-9]+\.[0-9]+
Required
Only When barcoding
Examples
-
1.0

The overall quality score given to the barcode detected. If barcoding was not performed for the read a value of - is used.

barcode_front_score

Regex -|-?[0-9]+\.[0-9]+
Required
Only When barcoding
Examples
-
1.0

The quality score given to the front barcode detected. If barcoding was not performed for the read a value of - is used.

barcode_front_foundseq_length

Regex -|[0-9]+
Required
Only When barcoding
Examples
-
20

The length of the front barcode found. If barcoding was not performed for the read a value of - is used.

barcode_front_begin_index

Regex -|[0-9]+
Required
Only When barcoding
Examples
-
0

The base index in the sequence the front barcode began. If barcoding was not performed for the read a value of - is used.

barcode_rear_score

Regex -|-?[0-9]+\.[0-9]+
Required
Only When barcoding
Examples
-
1.0

The quality score given to the read barcode detected. If barcoding was not performed for the read a value of - is used.

barcode_rear_foundseq_length

Regex -|[0-9]+
Required
Only When barcoding
Examples
-
10

The length of the rear barcode found. If barcoding was not performed for the read a value of - is used.

barcode_rear_end_index

Regex -|[0-9]+
Required
Only When barcoding
Examples
-
0

The base index in the sequence the front barcode began. If barcoding was not performed for the read a value of - is used.

alignment_genome

Regex \+|-|\*|[A-Za-z0-9\-_\.]+
Required
Only When aligning
Examples
-
Lambda

The genome the read was aligned to. If alignment was not performed for the read a value of - is used.

alignment_direction

Regex \+|-|\*
Required
Only When aligning
Examples
-
+
*

The direction of the alignment. If alignment was not performed for the read a value of - is used.

alignment_genome_start

Regex -|[0-9]+
Required
Only When aligning
Examples
0

The start position of the alignment on the genome. If alignment was not performed for the read a value of - is used.

alignment_genome_end

Regex -|[0-9]+
Required
Only When aligning
Examples
-
100

The end position of the alignment on the genome. If alignment was not performed for the read a value of - is used.

alignment_strand_start

Regex -|[0-9]+
Required
Only When aligning
Examples
-
0

The start position of the alignment on the strand. If alignment was not performed for the read a value of - is used.

alignment_strand_end

Regex -|[0-9]+
Required
Only When aligning
Examples
-
100

The end position of the alignment on the strand. If alignment was not performed for the read a value of - is used.

alignment_num_insertions

Regex -|-1|[0-9]+
Required
Only When aligning
Examples
-
4

The number of insertions in the alignment. If alignment was not performed for the read a value of - is used.

alignment_num_deletions

Regex -|-1|[0-9]+
Required
Only When aligning
Examples
-
1

The number of deletions in the alignment. If alignment was not performed for the read a value of - is used.

alignment_num_aligned

Regex -|-1|[0-9]+
Required
Only When aligning
Examples
-
100

The number of aligned bases in the alignment. If alignment was not performed for the read a value of - is used.

alignment_num_correct

Regex -|-1|[0-9]+
Required
Only When aligning
Examples
-
100

The number of correct bases in the alignment. If alignment was not performed for the read a value of - is used.

alignment_identity

Regex -|-?[0-9]+\.[0-9]+
Required
Only When aligning
Examples
-
0.99

The identity score of the alignment. If alignment was not performed for the read a value of - is used.

alignment_accuracy

Regex -|-?[0-9]+\.[0-9]+
Required
Only When aligning
Examples
-
0.99

The accuracy of the alignment. If alignment was not performed for the read a value of - is used.

alignment_score

Regex -|-?[0-9]+
Required
Only When aligning
Examples
-
4

The score assigned to the alignment. If alignment was not performed for the read a value of - is used.

alignment_coverage

Regex -|-?[0-9]+\.[0-9]+
Required
Only When aligning
Examples
-
0.99

The coverage of the alignment. If alignment was not performed for the read a value of - is used.

alignment_bed_hits

Regex -|[0-9]+
Required
Only When aligning
Examples
-
1

The number of hits in the alignment BED file. If alignment was not performed for the read a value of - is used.

alignment_mapping_quality

Regex -|[0-9]+
Required
Only When aligning
Examples
-
1

The mapping quality of the alignment. If alignment was not performed for the read a value of - is used.

alignment_num_alignments

Regex -|[0-9]+
Required
Only When aligning
Examples
-
1

The number of alignments found for the read. If alignment was not performed for the read a value of - is used.

alignment_num_secondary_alignments

Regex -|[0-9]+
Required
Only When aligning
Examples
-
2

The number of secondary alignments found for the read. If alignment was not performed for the read a value of - is used.

alignment_num_supplementary_alignments

Regex -|[0-9]+
Required
Only When aligning
Examples
-
3

The number of supplementary alignments found for the read. If alignment was not performed for the read a value of - is used.

duplex_parent_template

Regex -|[a-f0-9]{8}-[a-f0-9]{4}-[4-5][a-f0-9]{3}-[89ab][a-f0-9]{3}-[a-f0-9]{12}
Required
Only When duplex
Examples
e4994c62-93f9-439a-bc8f-d20c95a137a5

The parent read id of the template read.

duplex_parent_complement

Regex -|[a-f0-9]{8}-[a-f0-9]{4}-[4-5][a-f0-9]{3}-[89ab][a-f0-9]{3}-[a-f0-9]{12}
Required
Only When duplex
Examples
e4994c62-93f9-439a-bc8f-d20c95a137a5

The parent read id of the complement read.