Pipeline DnapipeTE

Short description

Dependancies

• singularity : needed for running the image of dnapipeTE (should be in $PATH)
• conda/snakemake
• NSDPY : pip install nsdpy (should be in $PATH)

Before first run

Download contamination database

• Download from NCBI the sequences corresponding to the querry in database_mito_conta/conta_sequence_refseq.search
• put the file in database_mito_conta as conta_sequence_refseq.fasta.gz

Prepare RepeatMasker + RepBase updated library

• put Dfam.h5 in RepBase/tmp_repbase/
• extract RMRBSeqs.embl from RepBaseRepeatMaskerEdition-#######.tar.gz
• put RMRBSeqs.embl in RepBase/tmp_repbase/

Run the snakemake rule initialise

This rule will :

• Download the mitochondrial database
• Download dnapipe_utils (for making graph in the end of the pipeline)
• Download tools for the pipeline (UrQt)
• Create a new RepeatMasker library with RepBase
• Create dnapipeTE singularity image

snakemake initialise -j 5

Run the pipeline

snakemake all --use-conda -j 16 -C genome_size=$GENOME_SIZE \
 sampling_size=$SAMPLING \
 out_dir=$OUTDIR \
 short_reads=$SR \
 species=$SPECIES \
 acc_num=$ACNUM

 example :
 snakemake all --use-conda -j 16 -C genome_size=199491796 \
  sampling_size="0.25" \
  out_dir="/beegfs/project/nega/dnapipe/Drosophila_pseudoobscura/dnapipe_025" \
  short_reads="/beegfs/data/gdebaecker/Drosophila_pseudoobscura/short_reads/SRR11813283_1.fastq.gz" \
  species="D_pseudoobscura" \ 
  acc_num="SRR11813283"

To do

• name
• description
• script auto

DAG of the pipeline