human_minimap2_extra_params.toml

# Summary: This example configuration demonstrates passing additional parameters through to the aligner.
# These parametes can be used to fine tune the alignment process.
# In this case we are setting the best_n parameter to 1, which will
# cause mappy to only report the best alignment for each read.
# This is useful for reducing the size of the output file.
# See the mappy documentation (https://github.com/lh3/minimap2/tree/master/python)
# for more details on the parameters that can be passed through.
# This example is configured for running with r10.4.1 flowcells and 5khz sample rate.


# Genomic targets are specified directly in the toml file in the form
#   "contig"
# or as:
#   "contig,start,end,strand"
# for example, "chr2,0,100,+"" or "chr2".
# If chr2 is specified, the entire contig will be considered a target, on both strands.
# These patterns can be mixed, both in the toml or in a .csv file.


# All of the below fields are explained in more detail in the documentation -
# https://looselab.github.io/readfish/toml.html

# Basecaller configuration
[caller_settings.guppy]
#               ^^^^^^ - ".guppy" specifies our chosen basecaller
# Guppy base-calling configuration file name
config = "dna_r10.4.1_e8.2_400bps_5khz_fast"
# Address of the guppy basecaller - The default address for guppy is ipc:///tmp/.guppy/5555.
address = "ipc:///tmp/.guppy/5555"
# Fastq output for individual reads. This is OPTIONAL - as these files can become quite large.
# Remove line to disable.
debug_log = "live_reads.fq"

# Aligner Configuration
[mapper_settings.mappy]
#               ^^^^^^ - ".mappy" specifies mappy as the aligner.
# Use mappy_rs for the rust version (required on PromethION)
# Alignment reference to use. Should be either FASTA or an MMI
fn_idx_in = "/path/to/hg38.mmi"
# Optional PAF output for live alignments.
# Remove line to disable.
debug_log = "live_alignments.paf"
# Number of threads for indexing (mappy and mappy-rs) and mapping (mappy-rs only)
n_threads = 4
# Number of alignments to report for each read.
# As this parameter is not recognised by readfish, it is passed through to the mappy Aligner,
# when it is initialised.
best_n = 1

# Region Configuration - see https://looselab.github.io/readfish/toml.html#analysis-regions for more information.
# Definitions of "unblock", "proceed" and "stop_receivings" are as follows

    # proceed: Allow one more chunk to be captured, before trying to make another decision, i.e proceed for now

    # unblock: Unblock the read

    # stop_receiving: Allow the read to be sequenced, and stop receiving signal chunks for it.
# This region will enrich for reads mapping to chr20 and chr21.
[[regions]]
name = "hum_test"
min_chunks = 1 # minimum number of chunks before a decision can be made
max_chunks = 4 # maximum number of chunks to use in decision making - after this perform the above_max_chunks action
targets = ["chr20", "chr21"]  # Genomic targets for this region
single_on = "stop_receiving"  # Action to take if there is one mapping on target.
multi_on = "stop_receiving"   # Action to take if there is more than one mapping, with at least one target.
single_off = "unblock"        # Action to take if there is one mapping and it is off target
multi_off = "unblock"         # Action to take if there are multiple mappings, where all are off target.
no_seq = "proceed"            # Action to take if there is no sequence information
no_map = "proceed"            # Action to take if there is no mapping information
above_max_chunks = "unblock"  # Action to take if the number of chunks received is above max_chunks
below_min_chunks = "proceed"  # Action to take if the number of chunks received is below min_chunks