CoverageStats

Calculate coverage statistics after mapping short-read sequenced isolates to a reference sequence

Installation of package

git clone https://github.com/kylegontjes/CoverageStats.git

Before running the pipeline

1. Set up the reference genome

Approach #1: Helper script

bash index_reference_genome.sh [reference_genome.fasta]

Approach #2: Manual curation

A. Create index of reference genome

module load Bioinformatics

module load bwa

bwa index [reference_genome.fasta]

B. Create fai index file

module load samtools

samtools faidx [reference_genome.fasta]

C. Create sequence dictionary

module load gatk

gatk CreateSequenceDictionary -R [reference_genome.fasta]

2. Generate isolate list

path="/nfs/esnitkin/Project_Penn_KPC/Sequence_data/fastq/Penn/SRA_submission/"

sample_id="sample_id"

sample_names=$(ls -1 $path | grep _R1 | cut -d. -f1 | sed 's/_R1//')

echo -e\n $sample_id $sample_names | tr ' ' '\n' > config/sample.tsv

3. Edit the config/cluster.json file with your account, email address (email), and desired walltime (walltime)

4. Update the config/config.yaml or config/config_pretrimmed.yaml with sample list (samples), results folder name (prefix), input reads' path (input_reads), and the reference genome's path (reference_genome)

Running snakemake workflow

module load singularity module load snakemake

Dry run

snakemake -s CoverageStats.smk --dryrun -p

Preferred method: Running sbat script

On non-trimmed files

sbatch CoverageStats.sbat

On pre-trimmed files

sbatch CoverageStats_pretrimmed.sbat

Alternative method: Run command in terminal as interactive job

On non-trimmed files

snakemake -s CoverageStats.smk --use-singularity -j 999 --cluster "sbatch -A {cluster.account} -p {cluster.partition} -N {cluster.nodes} -t {cluster.walltime} -c {cluster.procs} --mem-per-cpu {cluster.pmem} --output=slurm_out/slurm-%j.out" --cluster-config config/cluster.json --configfile config/config.yaml --latency-wait 30 --keep-going

On pre-trimmed files

snakemake -s CoverageStats_pretrimmed.smk --use-singularity -j 999 --cluster "sbatch -A {cluster.account} -p {cluster.partition} -N {cluster.nodes} -t {cluster.walltime} -c {cluster.procs} --mem-per-cpu {cluster.pmem} --output=slurm_out/slurm-%j.out" --cluster-config config/cluster.json --configfile config/config_pretrimmed.yaml --latency-wait 30 --keep-going