guppy_basecaller --disable_pings --compress_fastq -c dna_r9.4.1_450bps_fast.cfg -i flongle_fast5_pass/ -s flongle_test2 -x 'auto' --recursive 
Curtis Kapsak kapsakcj
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toniher
/ singularity-predownload.sh
Last active
March 24, 2023 15:35
Simple script for predownloading Singularity images in order to be convenient to be used by Nextflow. Useful for issues like this: https://github.com/nextflow-io/nextflow/issues/1210
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| #!/usr/bin/env bash | |
| CONFILE=${1:-nextflow.config} | |
| OUTDIR=${2:-./singularity} | |
| if [ ! -e $CONFILE ]; then | |
| echo "$CONFILE does not exist" | |
| exit | |
| fi |
sirselim
/ basecalling_notes.md
Last active
August 16, 2024 07:37
a collection of my notes while working on nanopore basecalling on the Jetson Xavier
awitney
/ gist:60b49d0a2cb8ab74d3376f955ee03721
Created
January 11, 2019 21:26
mycobacterium build kraken db
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| rsync -avL rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycobacterium_* refseq/Mycobacterium/ | |
| rsync -avL rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycolicibacterium_* refseq/Mycolicibacterium/ | |
| mkdir fna | |
| find refseq/Mycobacterium/ -name "*_genomic.fna.gz" -exec cp {} fna \; | |
| find refseq/Mycolicibacterium/ -name "*_genomic.fna.gz" -exec cp {} fna \; | |
| rm -f fna/*_cds_from_genomic.fna.gz | |
| rm -f fna/*_cds_from_genomic.fna.gz | |
| rm -f fna/*_rna_from_genomic.fna.gz |
rxaviers
/ gist:7360908
Last active
December 17, 2025 18:15
Complete list of github markdown emoji markup
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