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.