chunk_size arg Stride intervals per chunk. builtin_scripts arg Whether to use GPU kernels that were x arg Specify basecalling device: 'auto', or k arg Path to GPU kernel files location (only as_num_scalers arg Number of parallel scalers for adapter as_reads_per_runner arg Maximum reads per runner for adapter as_cpu_threads_per_scaler arg Number of CPU worker threads per adapter as_ gpu_runners_per_device arg Number of runners per GPU device for as_model_file arg Path to JSON model file for adapter pt_minimum_read_start_index arg Set minimum index for read start sample pt_required_adapter_ drop arg Set minimum required current drop from
adapter_pt_range_scale arg Set polyT/adapter range scale for setting pt_median_offset arg Set polyT median offset for setting read pt_scaling Enable polyT/adapter max detection for read jump_threshold arg Threshold level for rna stall detection dmean_threshold arg Threshold for coarse stall event detection dmean_win_size arg Window size for coarse stall event
trim_strategy arg Trimming strategy to apply: 'dna' or ' rna'
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scaling_mad arg Median absolute deviation to use for manual scaling_med arg Median current value to use for manual override_scaling Manually provide scaling parameters rather max_search_len arg Maximum number of samples to search through trim_min_events arg Adapter trimmer minimum stride intervals trim_threshold arg Threshold above which data will be trimmed : Guppy Basecalling Software, (C) Oxford Nanopore Technologies, Limited. Next up in the random nanopore read comparison: Bonito 0.1.5 vs Guppy 3.6.0: Bonito (left) seems to have a slightly higher accuracy due to fewer inserton/delitions but guppy maps a few more bases at the end of the read. Guppy 3.6.0 is a marked improvement for PromethION R9.4.1 data!!! Looking forward to the new announcements at LC2020!!! /wofInG39Be At this pace, it will look like reads in another 2 years! /FfIrYQnUAz Who knew I'd actually see the improved accuracy by eye 😮. I got back into some sequencing data I had from 2018 and ran basecalling again.
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