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@nathanhaigh
nathanhaigh / deinterleave_fastq.sh
Last active January 22, 2024 15:25
deinterleave FASTQ files
#!/bin/bash
# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress]
#
# Deinterleaves a FASTQ file of paired reads into two FASTQ
# files specified on the command line. Optionally GZip compresses the output
# FASTQ files using pigz if the 3rd command line argument is the word "compress"
#
# Can deinterleave 100 million paired reads (200 million total
# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s)
#
@fedarko
fedarko / gh_url_to_raw_gh_url.py
Created October 2, 2019 22:10
Convert a github file URL to a raw.githubusercontent.com URL (that can be directly accessed for things like view.qiime2.org or wget)
# your link goes here
link = "https://github.com/knightlab-analyses/qurro-mackerel-analysis/blob/master/AnalysisOutput/qurro-plot.qzv"
# note: this will break if a repo/organization or subfolder is named "blob" -- would be ideal to use a fancy regex
# to be more precise here
print(link.replace("github.com", "raw.githubusercontent.com").replace("/blob/", "/"))
# example output link:
# https://raw.githubusercontent.com/knightlab-analyses/qurro-mackerel-analysis/master/AnalysisOutput/qurro-plot.qzv