added genome assembly scripts & description

01-assembly/README.md

+# Genome assembly
+
+Code in this folder covers the steps from receiving the data until producing a favored draft
+assembly for scaffolding.
+
+### Preprocessing
+
+To estimate genome size, we counted kmers for the [ONT](preprocess-jellyfish_count-ont.sh) and
+[PacBio](preprocess-jellyfish_count-pb.sh) data using $k=21$. The resulting k-mer spectra were
+analyzed with [GenomeScope](http://genomescope.org) and
+[GenomeScope2](http://genomescope.org/genomescope2.0/).
+
+### Assembly
+
+The sequencing coverage was enough for robust genome size estimates (and also ONT data is
+technically not meant for k-mer spectrum analysis because of the high error rates). Since some
+genome assemblers require an estimated genome size, we assumed a genome size around 500Mb.
+
+We tried out a variety of assemblers, mostly on the ONT data.
+
+- [canu v2.2](assemble-canu.sh) (ONT)
+- [flye v2.9.2](assemble-flye.sh) (ONT)
+- [shasta v.0.11.1](assemble-shasta.sh) (ONT)
+- [Verkko v2.0](assemble-verkko.sh) (ONT)
+- [NextDenovo v2.5.2](assemble-nextdenovo.sh) (ONT)
+- [flye v2.9.2](assemble-flye-pb.sh) (PacBio)
+- [hifiasm v0.19.8](assemble-hifiasm.sh) (PacBio)
+
+
+### Evaluation
+
+Multiple tools failed, or required such extensive troubleshooting that we decided against using
+them. We performed basic QC on each finished assembly with the
+[`evaluate_assemblies.sh`](evaluate_assemblies.sh) script.
+
+- basic statistics with `quast`,
+- assessed completeness of metazoan and arthropod single-copy ortholog genes with `BUSCO`,
+- mapped available RNA-seq data onto the assembly,
+- mapped the ONT and PacBio data back to the assembly.
+
+The best assembly, in terms of contiguity and BUSCO completeness, was produced by Flye using the ONT
+data; this assembly was kept for further work.

01-assembly/assemble-canu.sh

+#!/usr/bin/env bash
+#
+#SBATCH --job-name=canu_pycno
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=30
+#SBATCH --mem=100G
+#SBATCH --time=48:00:00
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=nikolaos.papadopoulos@univie.ac.at
+#SBATCH --output=/lisc/user/papadopoulos/log/pycno-canu-%j.out
+#SBATCH --error=/lisc/user/papadopoulos/log/pycno-canu-%j.err
+
+module load assembly/canu/2.2
+
+# long read input
+NANOPORE="/lisc/scratch/zoology/pycnogonum/raw/20230601_0904_3C_PAK64436_4d39d6a6/basecalls/202306050/PAK64436_1_202306050.fastq.gz"
+
+# output directory
+OUTPUT="/lisc/scratch/zoology/pycnogonum/genome/canu_full/"
+mkdir -p "$OUTPUT" || exit 1
+
+# go to $TMPDIR
+cd "$TMPDIR" || exit 1
+
+# run canu
+canu \
+ -p ecoli \
+ -d ecoli-oxford \
+ genomeSize=550m \
+ maxMemory=100g \
+ maxThreads=30 \
+ minReadLength=500 \
+ fast=true \
+ -nanopore $NANOPORE
+
+# copy all the relevant output to the output directory
+cp -r "$TMPDIR"/ "$OUTPUT"
+
+# remove $TMPDIR
+cd "$OUTPUT" || exit 1
+rm -rf "$TMPDIR"
\ No newline at end of file

01-assembly/assemble-flye-pb.sh

+#!/usr/bin/env bash
+#
+#SBATCH --job-name=flye_pycno
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=16
+#SBATCH --mem=50G
+#SBATCH --time=10:00:00
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=nikolaos.papadopoulos@univie.ac.at
+#SBATCH --output=/lisc/user/papadopoulos/log/pycno-flye-%j.out
+#SBATCH --error=/lisc/user/papadopoulos/log/pycno-flye-%j.err
+
+module load conda
+conda activate flye-2.9.5
+
+HIFI="/lisc/scratch/zoology/pycnogonum/raw/m64120_240312_152428.ccs.fasta"
+OUTPUT=/lisc/scratch/zoology/pycnogonum/genome/flye_pb/
+
+mkdir -p $OUTPUT
+
+# Run Flye
+flye --pacbio-hifi $HIFI \
+--threads 16 \
+--out-dir $OUTPUT

01-assembly/assemble-flye.sh

+#!/usr/bin/env bash
+#
+#SBATCH --job-name=flye_pycno
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=30
+#SBATCH --mem=100G
+#SBATCH --time=10:00:00
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=nikolaos.papadopoulos@univie.ac.at
+#SBATCH --output=/lisc/user/papadopoulos/log/pycno-flye-%j.out
+#SBATCH --error=/lisc/user/papadopoulos/log/pycno-flye-%j.err
+
+module load conda
+conda activate flye-2.9.2
+
+NANOPORE="/lisc/scratch/zoology/pycnogonum/raw/20230601_0904_3C_PAK64436_4d39d6a6/basecalls/202306050/PAK64436_1_202306050.fastq.gz"
+OUTPUT=/lisc/scratch/zoology/pycnogonum/genome/flye_full/
+
+mkdir -p $OUTPUT
+
+# Run Flye
+flye --nano-raw $NANOPORE \
+--threads 30 \
+--out-dir $OUTPUT

01-assembly/assemble-hifiasm.sh

+#!/usr/bin/env bash
+#
+#SBATCH --job-name=flye_hifiasm
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=32
+#SBATCH --mem=50G
+#SBATCH --time=16:00:00
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=nikolaos.papadopoulos@univie.ac.at
+#SBATCH --output=/lisc/user/papadopoulos/log/pycno-hifiasm-%j.out
+#SBATCH --error=/lisc/user/papadopoulos/log/pycno-hifiasm-%j.err
+
+module load hifiasm/0.19.8
+
+HIFI="/lisc/scratch/zoology/pycnogonum/raw/m64120_240312_152428.ccs.fasta"
+# NANOPORE="/lisc/scratch/zoology/pycnogonum/raw/20230601_0904_3C_PAK64436_4d39d6a6/basecalls/202306050/PAK64436_1_202306050.fastq.gz"
+# OMNIC_R1="/lisc/scratch/zoology/pycnogonum/raw/omniC/DTG_OmniC_1016_R1.fastq"
+# OMNIC_R2="/lisc/scratch/zoology/pycnogonum/raw/omniC/DTG_OmniC_1016_R2.fastq"
+OUTPUT=/lisc/scratch/zoology/pycnogonum/genome/hifiasm/
+
+mkdir -p $OUTPUT
+
+hifiasm -o $OUTPUT/asm -t32 --primary $HIFI
\ No newline at end of file

01-assembly/assemble-nextdenovo.sh

+#!/usr/bin/env bash
+#
+#SBATCH --job-name=nextdenovo_pycno
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=20
+#SBATCH --mem=300G
+#SBATCH --time=168:00:00
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=nikolaos.papadopoulos@univie.ac.at
+#SBATCH --output=/lisc/user/papadopoulos/log/pycno-nextdenovo-%j.out
+#SBATCH --error=/lisc/user/papadopoulos/log/pycno-nextdenovo-%j.err
+
+module load conda
+conda activate nextdenovo
+
+# long read input
+NANOPORE="/lisc/scratch/zoology/pycnogonum/raw/20230601_0904_3C_PAK64436_4d39d6a6/basecalls/202306050/PAK64436_1_202306050.fastq.gz"
+# nextdenovo path
+nextdenovo="/lisc/user/papadopoulos/repos/NextDenovo/nextDenovo"
+# output directory
+OUTPUT="/lisc/scratch/zoology/pycnogonum/genome/nextdenovo_full/"
+mkdir -p "$OUTPUT" || exit 1
+
+# go to $TMPDIR
+cd "$TMPDIR" || exit 1
+
+# copy the nanopore reads to $TMPDIR
+cp $NANOPORE ./
+cp /lisc/user/papadopoulos/repos/NextDenovo/doc/pycno.cfg ./
+ls PAK64436_1_202306050.fastq.gz > input.fofn
+
+# run nextdenovo
+$nextdenovo pycno.cfg
+
+# copy all the relevant output to the output directory
+cp -r "$TMPDIR"/* "$OUTPUT"
+
+# remove $TMPDIR
+rm -rf "$TMPDIR"
\ No newline at end of file

01-assembly/assemble-shasta.sh

+#!/usr/bin/env bash
+#
+#SBATCH --job-name=shasta_pycno
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=48
+#SBATCH --mem=200G
+#SBATCH --time=5:00:00
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=nikolaos.papadopoulos@univie.ac.at
+#SBATCH --output=/lisc/user/papadopoulos/log/pycno-shasta-%j.out
+#SBATCH --error=/lisc/user/papadopoulos/log/pycno-shasta-%j.err
+
+SHASTA=/lisc/user/papadopoulos/bin/shasta-Linux-0.11.1
+
+NANOPORE="/lisc/scratch/zoology/pycnogonum/raw/20230601_0904_3C_PAK64436_4d39d6a6/basecalls/202306050/nanopore.fasta" # long read input
+OUTPUT="/lisc/scratch/zoology/pycnogonum/genome/shasta_full/" # output directory
+
+# run shasta
+$SHASTA --input $NANOPORE --assemblyDirectory $OUTPUT --threads 48 --config Nanopore-R10-Fast-Nov2022
+
+rm -rf "$TMPDIR"
\ No newline at end of file

01-assembly/assemble-verkko.sh

+#!/usr/bin/env bash
+#
+#SBATCH --job-name=verkko_controller
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=1G
+#SBATCH --time=30-00:00:00
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=nikolaos.papadopoulos@univie.ac.at
+#SBATCH --output=/lisc/user/papadopoulos/log/pycno-verkko-%j.out
+#SBATCH --error=/lisc/user/papadopoulos/log/pycno-verkko-%j.err
+
+module load conda
+conda activate verkko
+
+# long read input - ONT
+NANOPORE="/lisc/scratch/zoology/pycnogonum/raw/20230601_0904_3C_PAK64436_4d39d6a6/basecalls/202306050/PAK64436_1_202306050.fastq.gz"
+# long read input - PacBio CCS
+PACBIO=/lisc/scratch/zoology/pycnogonum/raw/m64120_240312_152428.ccs.fastq.gz
+
+# output directory
+OUTPUT="/lisc/scratch/zoology/pycnogonum/genome/verkko/"
+mkdir -p "$OUTPUT" || exit 1
+
+verkko -d $OUTPUT --hifi $PACBIO --nano $NANOPORE --local-cpus 1 --slurm --snakeopts "--cores 64 --jobs 10"
\ No newline at end of file

01-assembly/eval-backmap-ont.sh

+#!/usr/bin/env bash
+
+#SBATCH --job-name=backmap_pycno
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=16
+#SBATCH --mem=20G
+#SBATCH --time=15:00:00
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=nikolaos.papadopoulos@univie.ac.at
+#SBATCH --output=/lisc/user/papadopoulos/log/pycno-backmap-ont-%j.out
+#SBATCH --error=/lisc/user/papadopoulos/log/pycno-backmap-ont-%j.err
+
+module purge 
+
+module load samtools
+module load bedtools
+# module load bwa # only needed for short reads
+module load qualimap
+module unload R/4.2.3
+module load R
+module load perl/5.38.2
+export PERL5LIB="/lisc/user/papadopoulos/perl5/lib/perl5"
+
+module load conda
+conda activate minimap2-2.28
+
+cd "$TMPDIR" || exit
+
+ASSEMBLY=$1
+OUTPUT=$2
+mkdir -p "$OUTPUT" || exit
+NANOPORE="/lisc/scratch/zoology/pycnogonum/raw/20230601_0904_3C_PAK64436_4d39d6a6/basecalls/202306050/PAK64436_1_202306050.fastq.gz"
+BACKMAP="/lisc/user/papadopoulos/repos/backmap/backmap.pl"
+
+$BACKMAP -a "$ASSEMBLY" \
+-ont $NANOPORE \
+-o "$OUTPUT" \
+-t 16 \
+-qo "--java-mem-size=28G"
+
+# copy all the relevant output to the output directory
+cp -r "$TMPDIR"/*.bam "$OUTPUT"
+# delete $TMPDIR
+cd "$OUTPUT" || exit
+rm -rf "$TMPDIR"
+
+samtools stats -@ 16 *.bam > stats.txt
\ No newline at end of file

01-assembly/eval-backmap-pb.sh

+#!/usr/bin/env bash
+
+#SBATCH --job-name=backmap_pycno
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=16
+#SBATCH --mem=20G
+#SBATCH --time=15:00:00
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=nikolaos.papadopoulos@univie.ac.at
+#SBATCH --output=/lisc/user/papadopoulos/log/pycno-backmap-pacbio-%j.out
+#SBATCH --error=/lisc/user/papadopoulos/log/pycno-backmap-pacbio-%j.err
+
+module purge 
+
+module load samtools
+module load bedtools
+# module load bwa # only needed for short reads
+module load qualimap
+module unload R/4.2.3
+module load R
+module load perl/5.38.2
+export PERL5LIB="/lisc/user/papadopoulos/perl5/lib/perl5"
+
+module load conda
+conda activate minimap2-2.28
+
+cd "$TMPDIR" || exit
+
+ASSEMBLY=$1
+OUTPUT=$2
+mkdir -p "$OUTPUT"
+
+PACBIO="/lisc/scratch/zoology/pycnogonum/raw/m64120_240312_152428.ccs.fasta"
+BACKMAP="/lisc/user/papadopoulos/repos/backmap/backmap.pl"
+
+$BACKMAP -a "$ASSEMBLY" \
+-hifi $PACBIO \
+-o "$OUTPUT" \
+-t 16 \
+-qo "--java-mem-size=28G"
+
+# copy all the relevant output to the output directory
+cp -r "$TMPDIR"/*.bam "$OUTPUT"
+# delete $TMPDIR
+cd "$OUTPUT" || exit
+rm -rf "$TMPDIR"
+
+samtools stats -@ 16 *.bam > stats.txt
\ No newline at end of file

01-assembly/eval-busco.sh

+#!/usr/bin/env bash
+#
+#SBATCH --job-name=busco_pycno
+#SBATCH --cpus-per-task=16
+#SBATCH --mem=50G
+#SBATCH --time=6:00:00
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=nikolaos.papadopoulos@univie.ac.at
+#SBATCH --output=/lisc/user/papadopoulos/log/pycno-busco-%j.out
+#SBATCH --error=/lisc/user/papadopoulos/log/pycno-busco-%j.err
+
+module load conda
+conda activate busco-5.7.1
+
+RESDIR=$1
+FASTA=$2
+MODE=$3
+
+BUSCO="/lisc/scratch/zoology/db/busco/"
+
+# mkdir -p "$RESDIR"/busco_arthropoda || exit
+mkdir -p "$RESDIR"/busco_metazoa || exit
+cd "$TMPDIR" || exit
+
+# busco -i "$FASTA" -l arthropoda -m "$MODE" -o arthropoda -r -c 16 --offline --download_path $BUSCO
+busco -i "$FASTA" -l metazoa -m "$MODE" -o metazoa -r -c 16 --offline --download_path $BUSCO
+
+cd "$RESDIR" || exit
+# cp -r "$TMPDIR"/arthropoda ./busco_arthropoda/
+cp -r "$TMPDIR"/metazoa ./busco_metazoa/
+rm -rf "$TMPDIR"
\ No newline at end of file

01-assembly/eval-map_RNA.sh

+#!/usr/bin/env bash
+#
+#SBATCH --job-name=star_pycno
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=30
+#SBATCH --mem=30G
+#SBATCH --time=6:00:00
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=nikolaos.papadopoulos@univie.ac.at
+#SBATCH --output=/lisc/user/papadopoulos/log/pycno-star-%j.out
+#SBATCH --error=/lisc/user/papadopoulos/log/pycno-star-%j.err
+
+module load ngstools/star/2.7.11a
+
+FASTA=$1
+ASSEMBLY=$(dirname "$FASTA") # path to the genome directory where the STAR index was generated
+OUTPUT=$ASSEMBLY/transcriptome
+
+mkdir "$OUTPUT" -p || exit
+
+# first go into the assembly directory and create the STAR index
+cd "$ASSEMBLY" || exit
+
+# create the STAR index
+STAR --runThreadN 30 \
+--runMode genomeGenerate \
+--genomeDir "$ASSEMBLY" \
+--genomeFastaFiles "$FASTA" \
+--genomeSAindexNbases 13
+
+
+BASE="/lisc/scratch/zoology/pycnogonum/raw/HTT33DSX5_4_R15615_20230713/demultiplexed"
+
+EMBRYO3="$BASE/235255/235255_S49"
+INSTAR1="$BASE/235253/235253_S47"
+INSTAR6="$BASE/235254/235254_S48"
+INSTAR2="$BASE/235256/235256_S50"
+INSTAR3="$BASE/235257/235257_S51"
+INSTAR4="$BASE/235258/235258_S52"
+INSTAR5="$BASE/235259/235259_S53"
+JUV1="$BASE/235260/235260_S54"
+SUBADULT="$BASE/235261/235261_S55"
+
+# put them all in a list
+TRANSCRIPTOMES=("$INSTAR1" "$INSTAR6" "$INSTAR2" "$INSTAR3" "$INSTAR4" "$INSTAR5" "$JUV1" "$SUBADULT")
+
+R1="$EMBRYO3"_L004_R1_001.fastq.gz
+R2="$EMBRYO3"_L004_R2_001.fastq.gz
+
+# now loop through the list and concatenate the R1/R2 files
+for stage in "${TRANSCRIPTOMES[@]}"; do
+    R1=$R1,"$stage"_L004_R1_001.fastq.gz
+    R2=$R2,"$stage"_L004_R2_001.fastq.gz
+done
+
+cd "$TMPDIR" || exit
+
+STAR --runThreadN 30 \
+--genomeDir "$ASSEMBLY" \
+--readFilesIn "$R1" "$R2" \
+--readFilesCommand gunzip -c
+
+# copy relevant files
+mkdir "$OUTPUT" -p || exit
+
+cp -r "$TMPDIR"/Log.* "$OUTPUT"/
+cp -r "$TMPDIR"/Aligned.* "$OUTPUT"/
+
+# remove $TMPDIR
+rm -rf "$TMPDIR"
\ No newline at end of file

01-assembly/eval-quast.sh

+#!/usr/bin/env bash
+#
+#SBATCH --job-name=quast_pycno
+#SBATCH --cpus-per-task=1
+#SBATCH --mem=600M
+#SBATCH --time=10:00
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=nikolaos.papadopoulos@univie.ac.at
+#SBATCH --output=/lisc/user/papadopoulos/log/pycno-quast-%j.out
+#SBATCH --error=/lisc/user/papadopoulos/log/pycno-quast-%j.err
+
+module load conda
+conda activate quast-5.2.0
+
+ASSEMBLY=$1
+RESDIR=$2
+NAME=$3
+mkdir "$RESDIR" -p
+
+quast.py -t 1 \
+-l "$NAME" \
+-o "$RESDIR" \
+--gene-finding \
+--eukaryote \
+"$ASSEMBLY"
\ No newline at end of file

01-assembly/evaluate_assemblies.sh

+#!/usr/bin/env bash
+
+# This script is used to start all evaluation analysis for the different genome assemblies
+
+# keep track of our assemblies
+BASE="/lisc/scratch/zoology/pycnogonum/genome"
+FLYE=${BASE}/flye_full/assembly.fasta
+SCAFFOLD=${BASE}/draft/draft.fasta
+REPEATS=${BASE}/draft/draft_softmasked.fasta
+SHASTA=${BASE}/shasta_full/Assembly.fasta
+
+
+# put assemblies in an array
+ASSEMBLIES=("$SCAFFOLD")
+NAMES=("draft")
+
+# I will check three things for each assembly:
+# 1. BUSCO
+# 2. QUAST
+# 3. RNAseq mapping
+# 4. mapping to the Nymphon genome
+# 5. DNA backmapping
+
+##### Tools
+BUSCO=/lisc/user/papadopoulos/repos/pycno-seq/nanopore/eval-busco.sh
+QUAST=/lisc/user/papadopoulos/repos/pycno-seq/nanopore/eval-quast.sh
+STAR=/lisc/user/papadopoulos/repos/pycno-seq/nanopore/eval-map_RNA.sh
+BACKMAP_ONT=/lisc/user/papadopoulos/repos/pycno-seq/nanopore/eval-backmap-ont.sh
+BACKMAP_PB=/lisc/user/papadopoulos/repos/pycno-seq/pacbio/eval-backmap-pb.sh
+
+# loop over the assemblies and names and submit the evaluation jobs for each
+# use the appropriate name for each assembly
+for i in "${!ASSEMBLIES[@]}"; do
+  # BUSCO completeness
+  ASSEMBLY=${ASSEMBLIES[$i]}
+  RESDIR=$(dirname "$ASSEMBLY")
+  sbatch "$BUSCO" "$RESDIR" "$ASSEMBLY"
+
+  # quast for basic assembly qc stats
+  NAME=${NAMES[$i]}
+  RESDIR=$(dirname "$ASSEMBLY")
+  sbatch "$QUAST" "$ASSEMBLY" "$RESDIR"/quast "$NAME"
+
+  # map RNA reads with STAR
+  sbatch "$STAR" "$ASSEMBLY"
+  
+  # map the DNA reads to the assembly with backmap
+  RESDIR=$(dirname "$ASSEMBLY")/backmap/
+  sbatch $BACKMAP_ONT "$ASSEMBLY" "$RESDIR"/backmap/ont
+  sbatch $BACKMAP_PB "$ASSEMBLY" "$RESDIR"/backmap/pacbio
+done

01-assembly/preprocess-jellyfish_count-ont.sh

+#!/usr/bin/env bash
+#
+#SBATCH --job-name=jellyfish_pycno
+#SBATCH --cpus-per-task=16
+#SBATCH --mem=75G
+#SBATCH --time=1:30:00
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=nikolaos.papadopoulos@univie.ac.at
+#SBATCH --output=/lisc/user/papadopoulos/log/pycno-pre-jf-%j.out
+#SBATCH --error=/lisc/user/papadopoulos/log/pycno-pre-jf-%j.err
+
+module load jellyfish/2.3.0
+
+k=$1
+NANOPORE="/lisc/scratch/zoology/pycnogonum/raw/20230601_0904_3C_PAK64436_4d39d6a6/basecalls/202306050/nanopore.fasta"
+OUTPUT="/lisc/scratch/zoology/pycnogonum/genome/ont-jellyfish-k$k.res"
+
+cd "$TMPDIR" || exit 1
+
+jellyfish count -C -m "$k" -s 1000000000 -t 16 $NANOPORE -o reads.jf
+jellyfish histo -t 16 reads.jf > "$OUTPUT"
+
+# remove $TMPDIR
+cd "$OUTPUT" || exit 1
+rm -rf "$TMPDIR"
\ No newline at end of file

01-assembly/preprocess-jellyfish_count-pb.sh

+#!/usr/bin/env bash
+#
+#SBATCH --job-name=jellyfish_pycno
+#SBATCH --cpus-per-task=16
+#SBATCH --mem=50G
+#SBATCH --time=3:00:00
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=nikolaos.papadopoulos@univie.ac.at
+#SBATCH --output=/home/user/papadopoulos/log/pycno-pre-jf-%j.out
+#SBATCH --error=/home/user/papadopoulos/log/pycno-pre-jf-%j.err
+
+module load jellyfish/2.3.0
+
+k=$1
+PACBIO="/scratch/zoology/pycnogonum/raw/m64120_240312_152428.ccs.fasta"
+OUTPUT="/scratch/zoology/pycnogonum/genome/pb-jellyfish-k$k.res"
+
+cd "$TMPDIR" || exit 1
+
+jellyfish count -C -m "$k" -s 1000000000 -t 16 $PACBIO -o reads.jf
+jellyfish histo -t 16 reads.jf > "$OUTPUT"
+
+# remove $TMPDIR
+cd || exit 1
+rm -rf "$TMPDIR"
\ No newline at end of file