Quickstart

Requirements

quicksand has two dependencies

Nextflow:

Version 22.04 or above. See here

Container:

Please use Singularity or Docker

Tip

check the successful installation of the software by running:

nextflow -v
    >>> nextflow version 22.10
singularity --version
    >>> singularity version 3.7.2-dirty

Download the database

Download the most recent datastructure for running the quicksand pipeline here:

latest=$(curl http://ftp.eva.mpg.de/quicksand/LATEST)
wget -r -np -nc -nH --cut-dirs=3 --reject="*index.html*" -q --show-progress -P refseq http://ftp.eva.mpg.de/quicksand/build/$latest

This step takes a while! Make yourself a coffee and relax

Download test-data

As input for the pipeline, download the Hominin "Hohlenstein-Stadel" mtDNA [1] into a directory split:

wget -q --show-progress -P split http://ftp.eva.mpg.de/neandertal/Hohlenstein-Stadel/BAM/mtDNA/HST.raw_data.ALL.bam

Run quicksand

nextflow pipelines can be executed directly from github. To run quicksand using the downloaded data-set type:

nextflow run mpieva/quicksand -r v2.1 \
  -profile   singularity \
  --db       refseq/kraken/Mito_db_kmer22 \
  --genomes  refseq/genomes/ \
  --bedfiles refseq/masked/ \
  --split    split/
The output of quicksand can be found in the directory quicksand_v2.1/
See the final_report.tsv and filtered_report_0.5p_0.5b.tsv for a summary of the results.
See the Input and Output section for a detailed explaination of all the output files.