CamDavidsonPilon

{
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  "examples.download": true,
  "patch.linewidth": 0.5,
  "legend.fancybox": true,
  "axes.color_cycle": [
    "#30a2da",
    "#fc4f30",
    "#e5ae38",
    "#6d904f",

lh3

This is a small experiment on the alignment of ~50bp INDELs. The query sequences are shown in 0.01.fq below, where seq_ori is a 204bp sequence extracted from the human reference genome, seq_del54 contains a 54bp deletion in the middle, seq_del84 contains a 84bp deletion in a 120bp read, and seq_ins40 contains a 40bp insertion in a 140bp read. These four short sequences were mapped to the human reference genome with Bowtie2, BWA-MEM, LAST, Novoalign, SNAP and Stampy with default settings. Non-default scoring functions were also tested for Bowtie2 (--rdg 5,1 --rfg 5,1), BWA-MEM (-A2 -E1) and LAST (-r2 -q4). The output by various mappers/settings can be found in this gist. The following table gives my summary:

Mapper	Setting	-84bp	-54bp	+40bp
BBMAP	default	Yes	Yes	Yes
Bowtie2	default	No	No	No
Bowtie2	--rdg 5,1 --rfg 5,1	as insertion	as insertion	Yes
BWA-MEM	default	as split	Yes	Yes
BWA-MEM	-A2 -E1	Yes	Yes	Yes
LAST	default	as split	as split

lh3

#
# generate 01compositional.bed.gz
#

# low-complexity by mDUST
mdust hs37d5.fa -c -w7 -v28 \
  | hs37d5.mdust-w7-v28.txt \
  | cut -f1,3,4 \
  | gawk -vOFS="\t" '{--$2;print}' \
  | bgzip > 01compositional/hs37d5.mdust-w7-v28.bed.gz

17twenty

package main
import (
	"./binding"
	"fmt"
)

func main() {
	binding.PrintHello()
	binding.Seed(1)
	fmt.Println(binding.Random())

jmarshall

ARG  ubuntu_version=latest
FROM ubuntu:${ubuntu_version}

USER root

RUN apt-get update && apt-get install -y \
	build-essential \
	curl \
	git \
	libbz2-dev \

brwnj

# setting up AMI
sudo service docker stop
sudo rm -rf /var/lib/docker

# update the image
sudo yum update -y
sudo yum install -y mdadm
sudo yum install -y wget
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -f -p $HOME/miniconda

max-sixty

// This Zellij config offers a more modal experience than the default. There are
// very few keybindings in the mode that you spend most of your time in, and we
// need to hit `C-space` to go into a mode where we navigate.

// The only keybindings in the normal mode are:
// - `C-space` to go into the tmux mode
// - `C-n` for a new pane
// - `C-t` for a new tab
// - `A-[` & `A-]` to go to the previous/next tab
// - `S-arrow` to navigate between panes