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| Code Block |
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singularity exec -B /work/ont --nv docker://ghcr.io/eresearchqut/bonito:v0.0.3 bonito basecaller dna_r9.4.1_e8_sup@v3.3 \
. \
--modified-bases 5mC \
--reference /work/ont/reference/GCA_000001405.15_GRCh38_no_alt_analysis_set.mmi \
--recursive \
--alignment-threads 4 > basecalls_mod_ref_S.bam |
This example runs bonito from the container. It uses a particular folder with fast5 files (line 2)
Modified bases parameter 5mC (line 3)
Path to reference (line 4)
Search folder recursively (line 5)
Use threads and redirect STDOUT to a file (line 6)