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pythseq / basecalling_notes.md
Created March 15, 2021 15:35 — forked from sirselim/basecalling_notes.md
a collection of my notes while working on nanopore basecalling on the Jetson Xavier

Jetson Xavier basecalling notes

initial basecalling runs

'fast' flip-flop calling on the Jetson Xavier

guppy_basecaller --disable_pings --compress_fastq -c dna_r9.4.1_450bps_fast.cfg -i flongle_fast5_pass/ -s flongle_test2 -x 'auto' --recursive
@pythseq
pythseq / it-ebooks.md
Created February 5, 2021 09:53 — forked from baiwfg2/it-ebooks.md
Download ebooks as you want
@pythseq
pythseq / gist:38f9fbea6422bb48932f405920f4d93f
Created August 18, 2020 14:42 — forked from cschin/gist:4c09f2f6888703a6e1e57d782d3244e5
A note on evaluating genome assemblies with CHM13 BACs
+ bash getStats.sh chm13_pergrine_p_ctg_cns.fasta
Checking attempted with maximum distance from contig end of 1000 bp..Done
******************* BAC SUMMARY ******************
TOTAL : 341
BP : 51532183
************** Statistics for: chm13_p_ctg_cns.fasta ****************
BACs closed: 321 (94.1349); BACs attempted: 333 %good = 96.3964; BASES 48527269 (94.1689)
Median: 99.9878
MedianQV: 39.1364
Mean: 99.94864
@pythseq
pythseq / gnu-parallel-bioinformatics.md
Created August 18, 2020 14:40 — forked from Brainiarc7/gnu-parallel-bioinformatics.md
GNU Parallel usage in Bioinformatics with examples: A primer.
@pythseq
pythseq / orthomcl_tutorial.md
Created June 22, 2020 01:25 — forked from darencard/orthomcl_tutorial.md
Running OrthoMCL on a set of protein annotations

Running OrthoMCL on a set of protein annotations from various species

OrthoMCL is the leading piece of software for inferring orthologs across several organisms. In this tutorial I will provide detailed instructions for running a set of protein annotations through OrthoMCL.

Software and Data

  1. OrthoMCL, and it's dependencies, must be installed. Detailed information on this tool and its installation can be found here. I actually used a slightly modified version of OrthoMCL that was made available by the author of the orthomcl-pipeline (see below). There isn't much details on the ways this is different from the existing OrthoMCL, but this is available here.
  2. orthmcl-pipeline must also be installed, as this is how we will automate the OrthoMCL process. Detailed information on this tool and its installation can be found [here](https
@pythseq
pythseq / install-user-mosh.sh
Created April 29, 2020 02:28 — forked from ViViDboarder/install-user-mosh.sh
Mosh is great, but sometimes the remote server you're accessing doesn't have it installed or doesn't give you sudo access. This script will install mosh as a user.
#! /bin/bash
# Make a directory to hold local libs and bins
mkdir -p ~/usr/local
# Get protobuf
wget https://protobuf.googlecode.com/files/protobuf-2.5.0.tar.gz
# Extract protobuf
tar -xvzf protobuf-2.5.0.tar.gz
cd protobuf-2.5.0
@pythseq
pythseq / omicidx_example_metagenomics.R
Created April 26, 2020 00:38 — forked from seandavi/omicidx_example_metagenomics.R
library(tibble)
library(jsonlite)
library(curl)
as_tibble(jsonlite::fromJSON(curl('https://api.omicidx.cancerdatasci.org/sra/studies/ERP009142/runs?size=500'))$hits)
@pythseq
pythseq / test.smk
Created April 26, 2020 00:27 — forked from DonFreed/test.smk
An example Snakmake file with the DAG dependent target wildcards
#!/usr/bin/env snakemake
# Requires Python3.6 or greater
rule align_A:
output:
outfile = "align__A/{sample}.bam"
shell:
'''
mkdir -p $(dirname {output.outfile})
@pythseq
pythseq / finddups.nf
Created March 5, 2020 14:56 — forked from lindenb/finddups.nf
workflow nextflow finding duplicated files and creating a bash script to replace the duplicate with a symbolic link
params.directories="."
params.headsize=100000
params.extensions="bam bai"
params.help=false
params.extrafind=""
params.lines = 1000
params.publishDir="."
def helpMessage() {
log.info"""
@pythseq
pythseq / somalier.nf
Created January 17, 2020 07:55 — forked from lindenb/somalier.nf
nextflow workflow for somalier #nextflow #workflow #somalier #relatedness #samples #bam
params.prefix="output."
params.bamlist=""
params.sites="https://github.com/brentp/somalier/files/3412453/sites.hg19.vcf.gz"
params.help=false
params.pedigree="NO_FILE"
def helpMessage() {
log.info"""
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