Curtis Kapsak kapsakcj
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kapsakcj
/ gist:58fc633468e1d39a0ca51ee24ce464d5
Created
September 21, 2023 16:21
translate-PNUSA-to-SRR.txt
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| # jotting down so I don't forget this one! | |
| # originally shared from Erin Young | |
| # requires NCBI e-utils commands | |
| esearch -db sra -query $PNUSA </dev/null | efetch -format docsum | xtract -pattern Runs -element Run@acc |
kapsakcj
/ concatenate-barcoded-nanopore-reads.sh
Last active
March 7, 2025 06:56
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| #!/bin/bash | |
| # by: Curtis Kapsak ([email protected]) | |
| # 2021-07-30; updated 2022-03-03 | |
| # | |
| # This script is for concatenating fastq.gz files that from a Nanopore sequencing run, | |
| # specifically with barcoded/multiplexed sequencing runs. It will not overwrite the original fastq files, but rather | |
| # concatenate fastqs for each barcoded sample, and write them to a single output directory. | |
| # | |
| # REQUIREMENTS: | |
| # This script requires that fastq.gz files are arranged in the normal output/directory |
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| soil = c("Collembola", "Earthworms", "Myriapoda", | |
| "Termites", "Ants", "Isopods", "Psuedoscorpion", | |
| "Oribatid mites", "Protura", "Enchytraeids", "Nematodes", | |
| "Tardigrades", "Arbuscular mycorrhiza","Ectomycorrhiza", | |
| "Fungi", "Nitrifiers", "Denitrifiers", "Archaea", "Bacteria", | |
| "Protists", "Proteobacteria", "Lichen","Enchytraeides", "Coleoptera", | |
| "Slugs", "Spiders", "Ascomycota", "Basidiomycota", "Algae","Bacteriodes", | |
| "Verrucomicrobia") # Generate names | |
| # install.packages("devtools") |
kapsakcj
/ Dockerfile-lyveset-2.0.1-ubuntu-bionic
Created
April 8, 2019 18:12
Dockerfile for installing lyveset-2.0.1 in a container with ubuntu-bioinic as base image
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| #Use ubuntu as base image | |
| FROM ubuntu:bionic | |
| # metadata | |
| LABEL base.image="ubuntu:bionic" | |
| LABEL version="1" | |
| LABEL software="Lyve-SET" | |
| LABEL software.version="2.0.1" | |
| LABEL description="LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations" | |
| LABEL website="https://github.com/lskatz/lyve-SET" |
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| license: gpl-3.0 |
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| license: gpl-3.0 |
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| license: gpl-3.0 |