Snakemake pipeline for QC of low-coverage skim-sequencing of G&T seq data
Expects reads to be in a directory called READS with filenames in the format: {sample}_cDNA_R[12].fastq.gz and {sample}_gDNA_R[12].fastq.gz
Modify the config file config.yaml to set run_name and choose min number of gDNA and cDNA reads (see example below).
First run the GenerateSamplesheet.smk pipeline which just runs fastp on the raw reads to count reads and generate a "samplesheet":
snakemake -j 100 -p --snakefile GenerateSamplesheet.smk --cluster-config cluter.json --latency-wait 60 --cluster "sbatch -p {cluster.partition} -c {cluster.c} --mem={cluster.memory} --job-name={cluster.J} --time={cluster.time}"
Then run the full pipeline:
snakemake -j 100 -p --snakefile SkimSeqQC.smk --cluster-config cluster.json --latency-wait 60 --cluster "sbatch -p {cluster.partition} -c {cluster.c} --mem={cluster.memory} --job-name={cluster.J} --time={cluster.time}"
Example config.yaml file:
run_name: PLATE_NAME
samplesheet: samplesheet.tsv
fastq_dir: "READS"
# Minimum gDNA read count to be passed to SPAdes
min_gDNA_read_count: 70000
# Minimum cDNA read count to be passed to Trinity
min_cDNA_read_count: 50000
# Minimum rRNA length to report in top blast hits vs pr2 DB
# This is the length of the blast alignment not the annotated gene
min_rRNA_blast_length: 500
# Interval to use for calculating random kmer uniquess (not currently reported in summary)
rku_gDNA_interval: 25000
rku_cDNA_interval: 25000
# Map gDNA reads against the corresponding genome assembly
map_gDNA: True
# Map cDNA reads against the corresponding genome assembly
map_cDNA: True
# Identity threshold for clustering transcriptome assembly
cdhit_identity_threshold: 0.98
# How many reads to classify using centrifuge [-u/--upto <int> stop after first <int> reads/pairs (no limit)]
centrifuge_upto: 1000000
# Paths to databases
bbduk_adapters: /ei/projects/e/e5f1ee13-d3bf-4fec-8be8-38c6ad26aac3/data/results/CB-GENANNO-476_DToL_Protists/Reference/bbmap/resources/adapters.fa
pr2_database: /ei/projects/e/e5f1ee13-d3bf-4fec-8be8-38c6ad26aac3/data/results/CB-GENANNO-476_DToL_Protists/Reference/databases/pr2/5.0.0/pr2_version_5.0.0_SSU_taxo_long.fasta
diamond_database: /ei/projects/e/e5f1ee13-d3bf-4fec-8be8-38c6ad26aac3/data/results/CB-GENANNO-476_DToL_Protists/Reference/databases/diamond/reference_proteomes.dmnd
taxonomy_database: /ei/projects/e/e5f1ee13-d3bf-4fec-8be8-38c6ad26aac3/data/results/CB-GENANNO-476_DToL_Protists/Reference/databases/taxdump/fullnamelineage.dmp
kraken2_database: /ei/projects/e/e5f1ee13-d3bf-4fec-8be8-38c6ad26aac3/data/results/CB-GENANNO-476_DToL_Protists/Reference/databases/kraken2/
centrifuge_database: /ei/projects/e/e5f1ee13-d3bf-4fec-8be8-38c6ad26aac3/data/results/CB-GENANNO-476_DToL_Protists/Reference/databases/centrifuge/centrifugedb
centrifuge_NT_database: /ei/public/databases/centrifuge/ncbi/nt_20200707/nt