16th October 2024
Re-write of the user manual, including the latest instructions and recommendations.
Jul 5 2023
ADS_S1016_v1_revJ_12Nov2020
English
5th July 2023
- Updated information for where to save alignment files in "Designing and running an experiment with adaptive sampling" to prevent errors in MinKNOW.
6th January 2023
"Designing and running an experiment with adaptive sampling":
- The section "If the reference FASTA is greater than 100 Mb, it is recommended to make it small enough to contain only the regions to be enriched or depleted" has been removed.
- In "Release caveats", the basecalling models used with Adaptive sampling have been corrected: the Fast model is used on the GridION, and the 'sketch' model is used on the MinION Mk1C.
26th May 2022
- Updated the release caveats in the 'Designing and running an experiment with adaptive sampling' section. We have also included information about the barcode balance feature here.
22nd December 2021
"Designing and running an experiment with adaptive sampling":
- All references to adaptive sampling on MinION Mk1C have been removed.
- In "Output files", the definition of sequence_length has been updated to "The number of bases in the read. For stop_receiving reads, this is the number of bases recorded until the decision was made to continue sequencing the rest of the read."
- In "Output files", the first sentence has been changed to "The files that MinKNOW outputs during a sequencing experiment are described in the MinKNOW protocol".
23rd July 2021
- In the "Considerations for experimental design" section, a note has been added about the difference in the algorithm for enrichment vs depletion: "For enrichment, at least 200 bases are required to pass through the pore before a decision is made to accept the strand. However in practice, due to MinKNOW read detection the number is typically ~450 bases for R9.4.1 chemistry. For depletion, the minimum number of bases required is ~450, but up to 4000 bases can be read before a strand is ejected."
- In "Designing and running an experiment with adaptive sampling", a note has been added on inputting .bed files: "Note that if you do not input a .bed file, then the entire FASTA/minimap2 index file will be used for enrichment or depletion."
- In the "Troubleshooting" section, several new FAQs have been added.
22nd July 2021
In the "Designing and running an experiment with adaptive sampling" and "Troubleshooting" steps, the name of the read_until.csv file has been updated to adaptive_sampling.csv
24th March 2021
- In the "Considerations for experimental design" section, amended the worked example to say "In this example, a user enriches for 25% of the sample with a read length of 8,400 bases."
- In the "Troubleshooting" section, added an FAQ about running adaptive sampling on the MinION Mk1C.
- Several amendments to the "Designing and running an experiment with adaptive sampling" section:
- Added instructions for subsetting a large FASTA file for use with the MinION Mk1C beta release of adaptive sampling.
- Amended the "Release caveats" to include the MinION Mk1C beta release.
- Amended the link to the EPI2ME Labs workflow in "If you are targeting an exome"
- Updated the location of the CSV file "read_until.csv" to "other_reports" in the run folder