bschiffthaler

#!/usr/bin/env bash

get_sra() {
  local __FASTQ="$1"

  local __OUT="$PWD"
  local __DOWNLOAD_THREADS=1

  # Allow downloading with multiple threads
  if [[ ! -z "${DOWNLOAD_THREADS+x}" ]]; then

bschiffthaler

Genome Annotation using MAKER

MAKER is a great tool for annotating a reference genome using empirical and ab initio gene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a de novo genome annotation for Boa constrictor in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.

Software & Data

Software prerequisites:

1. RepeatModeler and RepeatMasker with all dependencies (I used NCBI BLAST) and RepBase (version used was 20150807).
2. MAKER MPI version 2.31.8 (though any other version 2 releases should be okay).
3. [Augustus](http://bio

bschiffthaler

library(SNPediaR)
library(tidyverse)

# Original function has som issues with parsing that need fixing
getPages2 <- function (titles, verbose = FALSE, limit = 50, wikiParseFunction = identity, 
                       baseURL, format, query, ...) 
{
  if (missing(baseURL)) 
    baseURL <- "https://bots.snpedia.com/api.php"
  if (missing(format)) 

bschiffthaler

List all stopped containers

docker ps -a -f status=exited

Delete all stopped containers

docker rm $(docker ps -aq -f status=exited)