Which sequencing services provide the highest quality metadata?

Question

[Jeremy Leipzig]

Which sequencing labs have the highest standards in terms of providing wet lab protocols and bioinformatic metadata?

This is our wishlist of sequence metadata - we wouldn't expect all this but more than a sequence file on a thumb drive:

adapter_name
adapter_sequence
aliquots
analyte_type
barcoding_pooling_strategy
base_caller_name
base_caller_version
bfx_contact
body_site
capture_kit
capture_method
case_control_status
checksum
consent
date_of_request
date_of_sequencing
sequencing_group_sample_identifier
dna_qc_status
experiment_type
filename
filesize
filetype
flowcell_id
fragment_length
genome_reference
includes_spike_ins
instrument
is_paired_end
is_tumor
lab_contact
lane
library_name
library_preparation_kit_catalog_number
library_preparation_kit_name
library_preparation_kit_vendor
library_preparation_kit_version
library_selection
library_strand
library_strategy
metadata_last_modified_date
platform
project_id
provider_supplied_sample_identifier
read_group
read_group_name
read_length
relation
requestor_contact
sample_type
sequencing_center
sequencing_date
size_selection_range
spike_ins_concentration
spike_ins_fasta
submitter_id
target_capture_kit_catalog_number
target_capture_kit_name
target_capture_kit_target_region
target_capture_kit_vendor
target_capture_kit_version
tissue_type

[Jeremy Leipzig]

cross-ref https://www.reddit.com/r/bioinformatics/comments/7j2wh1/metadata_and_data_requirementsstandards_for/

Answer 1

[Kevin Blighe]

That's a big wish list. My experience tells me that services operating out of universities will be more flexible in helping you with this. Also, obviously, newer companies/services will be more flexible. As an idea, I once worked in a clinical genetics service as Lead Bioinformatician and we certainly could have provided all of this information to people using the service.

I also take note of your 'base_caller_name' and 'base_caller_version'. The base calling software always remains buried under the rug, even though base calls can change from one base caller version to the next. It's one of those 'forgotten' issues in bioinformatics.