21st June 2023
In "Configuring a GPU version of Guppy with MinKNOW for MinION or PromethION 2 Solo on Windows/Linux":
- For Windows, CUDA Toolkit 11.8 requirement has been added
- For Linux, the Troubleshooting section has been updated with clearer stepwise instructions
- An erroneous reference to guppyd-cpu has been removed
22nd May 2023
- Formatting correction in the "Barcoding/demultiplexing" section of the protocol, under the "The Guppy barcoder supports the following optional parameters" snippet.
- Correction in the "Barcoding/demultiplexing" section of the protocol, under "The regions of a barcode" snippet: The barcode sequence exception for 12a is in the Rapid PCR Barcoding Kit (SQK-RPB004).
15th May 2023
The sections "Configuring a GPU version of Guppy with MinKNOW for MinION or PromethION 2 Solo on Windows" and "Configuring a GPU version of Guppy with MinKNOW for MinION or PromethION 2 Solo on Linux" have been expanded, and two new configuration use cases have been added.
5th May 2023
"Installing a GPU version of Guppy with MinKNOW for MinION or PromethION 2 Solo" - a new instruction has been added for how to configure Guppy to use TCP and allow remote connections.
22nd March 2023
A number of new parameters have been added and removed:
"Setting up a run: configurations and parameters":
- Added Emit move tables (--moves_out)
- Removed Client connection timeout (--conn_timeout_ms), Server connection hostname and port (-p or --port), and Client ID (--client_id)
"Guppy basecall server":
- Added High priority read threshold (--high_priority_threshold), Medium priority read threshold (--medium_priority_threshold), Maximum IPC message block size (--max_block_size), Number of threads for IPC message handling (--ipc_threads)
- Added Basecall client-specific parameters.
- Changed guppy_basecaller to guppy_basecaller_client
"Expert settings" - added Beam cut (--beam_cut), Beam width (--beam_width), Adapter scaling model file (--as_model_file), Number of adapter scalers (--as_num_scalers), Reads per scaler (--as_reads_per_runner), CPU threads per adapter scaler (--as_cpu_threads_per_scaler), GPU adapter scaling runners per device (--as_gpu_runners_per_device), Num alignment threads (--num_alignment_threads), Num barcoding threads (--num_barcoding_threads), Num modified base basecaller threads (--num_base_mod_threads), Num read splitting threads (--num_read_splitting_threads), Num read splitting buffers (--num_read_splitting_buffers).
"Barcoding/demultiplexing":
- Added Detect mid-strand adapters (--detect_mid_strand_adapter), Minimum score for detection of adapters (--min_score_adapter), Minimum score for detection of mid strand adapters (--min_score_adapter_mid), Minimum score for detection of primers (--min_score_primer), Progress stats reporting frequency (--progress_stats_frequency), Trace catagory logs (--trace_category_logs), Trace domains config (--trace_domains_config), Disable pings (--disable_pings), Telemetry URL (--ping_url), Ping segment duration (--ping_segment_duration).
- Changed --additional_context_bases to additional_lamp_context_bases
"Alignment" - added Perform read filtering based on alignment (--alignment_filtering), BED file (--bed_file), Alignment type (--align_type), Progress stats reporting frequency (--progress_stats_frequency), Trace catagory logs (--trace_category_logs), Trace domains config (--trace_domains_config), Disable pings (--disable_pings), Telemetry URL (--ping_url), Ping segment duration (--ping_segment_duration).
5th January 2023
In "Guppy software overview" - "CPU and GPU basecalling with Guppy", a note has been added to say "Please note that Guppy is not currently compatible with CUDA 12.0 onwards."
16th November 2022
Updates for Guppy version 6.4.2 release:
- "Guppy software overview": mentioned that .fast5 file support is now removed; added mention of duplex chemistry support alongside 1D. Re-worded the CUDA requirements from "recommended" to "The Guppy software requires CUDA Compute Capability >6.1".
- "Quick start - Linux": in "General help command-line options", a new command has been added for when model versions are not required: `guppy_basecaller --print_workflows --skip_model_versions`
- "Setting up a run: configurations and parameters": a new flag (--alignment_filtering) has been included, and the descriptions of --min_qscore and --min_score_read_splitting have been updated.
- "Input and output files": the --fast5_out flag and any mention of .fast5 output has been removed; the "workspace" part of the save path has been removed. In "Summary file contents", the descriptions of "passes_filtering" and "sequence_length_template" have been updated, while "mad_template" has been removed.
- "Expert settings": the "--override_scaling" flag description has been updated, and two new flag descriptions added: "--load_scaling_info_from_read_files" and "--use_quantile_scaling"
- "Barcoding/demultiplexing": a new flag description ("--disable_trim_barcodes") has been added, and the description of "--ext_in" has been updated. The "Barcode trimming" section has also been updated with new instructions.
- "Alignment": references to "FASTQ/FASTA files" have been replaced with "input files".
- "Modified base calling": references to .fast5 file output have been removed.
- "Duplex basecalling": instructions have been added for performing duplex basecalling in Guppy.
31st October 2022
- "Installing a GPU version of Guppy with MinKNOW for MinION on Linux/Windows" - all the instructions have been removed, except "Setting GPU parameters for lower-memory graphics cards", as GPU installers are now available for Windows and Linux.
17th October 2022
"Installing a GPU version of Guppy with MinKNOW for MinION on Linux" - the command in step 4 has been corrected, and all mentions of guppyd have been updated to guppyd-cpu.
16th September 2022
"Installing a GPU version of Guppy with MinKNOW for MinION on Linux/Windows" - for Linux, the commands in steps 5 and 6 have been updated. For Linux and Windows, the instructions for "Make sure the archive version of Guppy runs on your machine" have been updated.
12th September 2022
- "Guppy software overview" - minor changes to information about GPU basecalling and the basecalling models available in Guppy.
"Downloads of Guppy - Linux"
- "Supported platforms for Guppy" - last paragraph has been changed to: "From version 6.1.0 onwards, Guppy no longer officially supports Ubuntu 16 or earlier, as that version of Ubuntu has reached its End of Life (EOL) date. It should still be possible to run the Guppy archive releases on that platform, although it is not explicitly supported."
- Installation commands have been updated.
"Quick start":
- "Required parameters" - the minimum required parameters have been updated to say "The configuration file to use".
- "Default parameters": "The basecall model will be set as High Accuracy (HAC)" has been removed.
- The example command-line entry has been updated to specify a HAC basecalling model.
- "Setting up a run: configurations and parameters" - the information in this section has been re-arranged in a different order, and more explanations have been added about the structure of a config file as well as the basecalling model types.
- "Installing a GPU version of Guppy with MinKNOW for MinION on Linux/Windows" - more information has been added to "Setting GPU parameters for lower-memory graphics cards" on configuring GPUs for Guppy.
- "FAQ and Troubleshooting" - the FAQ on basecalling short reads has been removed.
24th August 2022
Updates in line with the release of Guppy v6.3.2
- Version 6.3.2 supports both .fast5 and the new POD5 input file formats. Anywhere in the protocol that previously mentioned .fast5 input has been amended to say "read file input" or ".fast5/.pod5 input".
- In "Guppy software overview", notes have been added about the introduction of the POD5 file format.
"Setting up a run: configurations and parameters":
- The descriptions of the alignment reference file, .bam file output and methylation probability cutoff parameters have been updated.
- "Config files - selecting kit and flow cell": examples of deprecated config files have been removed.
"Input and output files":
- "Output formats": a new note has been added about grouping multiple input files from the same run_id into batches.
- "Contents of the output folder": the description of `fastq_runid_<run_id>_<batch_id>_<file_number>.fastq` has been updated
- "Summary file contents": num_events has been replaced with minknow_events
- The alignment_genome_start, alignment_genome_end, alignment_strand_start and alignment_strand_end argument descriptions have been updated to the value of 0 if no alignment was found.
"Guppy basecall server":
- More information has been added about what happens if the server fails to start due to being improperly configured.
"Expert settings":
- More information has been added to the Read batch size argument description.
"Barcoding/demultiplexing":
- The descriptions of the Records per FASTQ and BAM file indexing arguments have been updated.
- Barcode trimming is now ON by default.
- "Adding your own barcodes": the descriptiosn of the id_pattern, first_index and normalised_id_pattern arguments have been updated. In the Quick Start section, a new note has been added at Step 3 for when using more than 99 barcodes.
"Alignment":
- Two new optional parameters have been added: Minimap options and Max records per output file.
- A new section has been added for supported minimap2 options.
"Modified base calling":
- The introduction has been updated.
- In "Raw modified base table format", the example table has been updated.
- The "BAM file modified base format" section has been updated.
28th July 2022
- In "Guppy software overview", the basecalling accuracy figures have been removed, and instead the user is referred to the latest information at https://nanoporetech.com/accuracy
- In "Guppy software overview" - "CPU and GPU basecalling with Guppy", GPU compatibility with Windows has been added
- In "Downloads of Guppy - Windows", the GPU installer is now mentioned
- In "Duplex basecalling", the example model name has been corrected to dna_r10.4.1_e8.2_400bps_sup.cfg
30th March 2022
- In "Input and output files", the "Nested output folders" section has been updated
- In "Installing a GPU version of Guppy with MinKNOW for MinION on Linux/Windows", the "Setting GPU parameters for lower-memory graphics cards" section has been updated to include a note to restart the guppyd/Windows service after the settings have been updated.
- In "Expert settings", a new parameter for adding sample sheet has been described (`--sample_sheet`)
- In "Modified base calling", the Raw modified base table format and BAM file modified base format are described, while the .fast5 file modified base format is now deprecated.
2nd February 2022
- In "Installing a GPU version of Guppy with MinKNOW for MinION on Linux", a new step has been added: "Rename the existing override.conf file so that it does not override our new settings".
- In "Installing a GPU version of Guppy with MinKNOW for MinION on Windows", the names of some of the parameters in Step 5 have been updated.
15th December 2021
Updates for the release of Guppy v6.0.0
- "Downloads of Guppy - Linux":
- Updates to the installation process when installing from .rpm
- In "Setting custom GPU parameters in Guppy", an update has been made to the calculation required to determine the amount of GPU memory that Guppy will use: memory used (in bytes) = gpu_runners_per_device * chunks_per_runner * chunk_size * model_factor
- "Setting up a run: configurations and parameters":
- Added information about the following flags: alignment reference file (-a or --align_ref), read splitting (--do_read_splitting), read splitting depth (--max_read_split_depth), minimum read splitting score (--min_score_read_splitting), and .bam file indexing (--index)
- "Input and output files":
- Added a note: "If read splitting was performed, the FASTQ header will also include a parent_read_id={parent_read_id} field, where parent_read_id is the read_id of the original read from which this read was split."
- Added information on the additional columns that will be present in the output if the following arguments are used: --detect_adapter, --detect_primer, --trim_barcodes, trim_adapters, and trim_primers
- Added information about the extra columns that will be present in the sequencing summary file if alignment is enabled via the --align_ref argument: alignment_mapping_quality, alignment_num_alignments, alignment_num_secondary_alignments, alignment_num_supplementary_alignments
- "Guppy basecall server":
- Added information about the following optional flags when launching the basecall server: --allow_non_local and --use_tcp
- Added information about the flag for allowing non-local connections (--allow_non_local)
- "Barcoding/demultiplexing":
- In "Data features", the following flags were added or changed: --min_score_barcode_front, --min_score_barcode_rear, --min_score_barcode_mask, --min_score_barcode_mid, --detect_adapter, --detect_primer, --index, and --ext_in.
- In "Adding your own barcodes", updated the contents of the barcoding sub-folder in /data. Also, the Quick Start Guide instructions have been updated.
- Added a new sub-section: "Context-specific barcode specification"
- "Alignment":
- Added information about the new flag for BAM file indexing (--index)
- Added a new sub-section: "File conversion"
- In "Guppy toolkit", added a sub-section on Duplex basecalling
- "FAQ and Troubleshooting":
- Updated the CUDA_ERROR_OUT_OF_MEMORY error FAQ to include CUDA_ERROR_OUT_OF_MEMORY, CUBLAS_STATUS_ALLOC_FAILED, and CUBLAS_STATUS_EXECUTION_FAILED
- In "Advanced troubleshooting for Guppy crashes", added an extra step to reproduce the crash with tracing enabled.
- Removed references to 1D^2 basecalling from the general system requirements and "Ping information"
- Improvements to formatting; minor corrections
27th October 2021
- Added a new section, "Installing a GPU version of Guppy with MinKNOW for MinION on Windows"
- Added troubleshooting instructions in "Installing a GPU version of Guppy with MinKNOW for MinION on Linux"
11th September 2021
- In "Barcoding/demultiplexing", a typo has been corrected in the spelling of the optional parameter --require_barcodes_both_ends . Also, the minimum score for detection of mid-strand barcodes has been updated to 50.0
- In "Quick start", under "Default parameters", the default for Q-score filtering has been changed to ON.
- In "Calibration Strand detection", added information about the RNA calibration strand, and that Guppy detects the calibration strand that is associated with the basecall configuration being used.
9th September 2021
- In "Guppy software overview", specs have been added for GPU basecalling on Windows. CUDA requirements and the list of fully-supported NVIDIA GPUs have also been updated.
- In "Guppy features, settings and analysis", a new step has been added: "Installing a GPU version of Guppy with MinKNOW for MinION"
21st May 2021
In "Guppy software overview", the description of th super high accuracy (sup) model has been added. There is also new benchmarking data for the basecalling speed and accuracy of the three models on various sequencing devices.
20th May 2021
- In the "Guppy software overview" step and the "Guppy toolkit" section, "Modified base calling" step, updated the type of modified bases supported by Guppy to 5mC. The basecalling model used to call 5mC bases is renamed to dna_r9.4.1_450bps_modbases_5mc_hac.cfg
- In the "Guppy toolkit" section, "Barcoding/demultiplexing" step, corrected a mistake in the commands under "Adding your own barcodes", Step 5: Add the new barcodes to the FASTA file.
- In the "Guppy software overview" step, the "General system requirements for running Guppy" has been updated to require 2 GB of drive space for installation.
- In the "Guppy toolkit" section, "Barcoding/demultiplexing" step, the default value for the --min_score_mask parameter has been updated to 40
- In the "Setting up a run: configurations and parameters" step, the default values for the --reverse_sequence and --u_substitution parameters have been corrected to TRUE and FALSE (capitalised)
24th March 2021
- "Guppy features, settings and analysis" section, "Setting up a run: configurations and parameters" step: updated the Q-score filtering parameter to "disable_qscore_filtering": Flag to disable filtering of reads into pass/fail folders inside the output folder, based on their strand q-score. Also updated the information for the minimum qscore parameter ("min_qscore"): The default value for this varies by configuration: for faster models it is 7.0, roughly corresponding to an accuracy of 85%, and is higher for more accurate models. This should have a minimal impact on output.
- "Guppy features, settings and analysis" section, "Input and output files" step: updated the text under "Default output of FASTQ files" to mention the updated "disable_qscore_filtering" parameter.
- "Guppy features, settings and analysis" section, "Input and output files" step: updated the text under "Summary file contents" to mention the updated "disable_qscore_filtering" parameter.
- "Guppy features, settings and analysis" section, "Expert settings" step: added a new parameter for Nnoisiest-section scaling maximum read size ("noisiest_section_scaling_max_size")
- "Guppy toolkit" section, "Barcoding/demultiplexing" step: added two new parameters: BAM file output (bam_out) and FASTQ file output (fastq_out)
- "Guppy toolkit" section, "Alignment" step: added new BAM file output (bam_out) parameter
23rd December 2020
Update for v4.4.0:
- Changes to the minimum required version of CUDA for GPU versions of Guppy
- Ubuntu 20 support
- Centos 8 support
28th September 2020
Update for v4.2.2:
- Separation of the basecaller into standalone and client applications
- BAM file output from the basecaller
- Support for a proposed format for storing methylation information in BAM files
- Significant improvements to GPU barcode detection speed
- Improvements to gap penalties in barcode detection
- An optional new barcoding approach separating mask and barcode scores
- Changes to mid-strand barcode detection default value
- Invalid command-line arguments are now treated as errors
- Removed the guppy_basecaller_1d2 application
18th June 2020
Changes for the release of Guppy v4.0:
- Support for new barcoding kits
- Initial support for alignment as part of basecalling
- Support for filtering alignment results using BED files
- BAM output from guppy_aligner
1st April 2020
Restructuring of the protocol, including:
- New structure, with each aspect of data analysis in its own dedicated section
- More details included in Quick Start on required parameters and defaults
- More explanation of certain optional parameters
- More information on basecalling included in the introduction
19th March 2020
Updates for Guppy v3.5.1 release, including:
- Adapter scaling for R9.4.1 DNA basecalling
- Optional folder output structure that mimics the one produced by MinKNOW
- Archive releases for Ubuntu 16 aarch64
14th October 2019
Updates for Guppy v3.3 release, including:
- Support for FASTA input
- Mid-strand barcode detection
- New R9.4.1 basecaller models
- PromethION basecaller models for older firmware versions
14th October 2019
Updates for Guppy v3.3 release, including:
- Support for FASTA input
- Mid-strand barcode detection
- New R9.4.1 basecaller models
- PromethION basecaller models for older firmware versions
14th October 2019
Updates for Guppy v3.3 release, including:
- Support for FASTA input
- Mid-strand barcode detection
- New R9.4.1 basecaller models
- PromethION basecaller models for older firmware versions
14th October 2019
Updates for Guppy v3.3 release, including:
- Support for FASTA input
- Mid-strand barcode detection
- New R9.4.1 basecaller models
- PromethION basecaller models for older firmware versions
Changes to documentation in line with release Guppy 3.2 and document reorgnisation in Git
__Features of Guppy 3.2:__
- Resume basecalling added
- Modified basecalling (in Output of Guppy basecalling in Setting, features and analysis).
__Other changes: __
- Matched to canonical source (Git)
- Rearranged to present features in sections towards end of document. Bascaller, Toolbox and Appendices
- FAQ and troubleshooting added
RevM
Changes to documentation in line with release Guppy 3.1.5
- Higher-confidence barcoding requiring matches at both ends
- An initial version of barcoding integrated with basecalling
- Support for reading and writing gzip-compressed FASTQ files
RevL
Changes to documentation in line with release Guppy 3.1.5
- Higher-confidence barcoding requiring matches at both ends
- An initial version of barcoding integrated with basecalling
- Support for reading and writing gzip-compressed FASTQ files
RevL
Changes to documentation in line with release Guppy 3.0.0
- End of Life for Ubuntu 14
- Updating GPU-drivers
- Update to Flip-flop model - e.g. 'Fast'/'HAC' config file replace the generic Flip-flop config file
RevK
Changes to documentation in line with release Guppy 3.0.0
- End of Life for Ubuntu 14
- Updating GPU-drivers
- Update to Flip-flop model - e.g. 'Fast'/'HAC' config file replace the generic Flip-flop config file
RevK