igordot / Sns
Licence: mit
Analysis pipelines for sequencing data
Stars: ✭ 43
Programming Languages
shell
77523 projects
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Seq-N-Slide: sequencing data analysis pipelines
Automated workflows for common sequencing-based (Illumina) protocols, such as RNA-seq, ChIP-seq, ATAC-seq, WGBS/RRBS methylation, whole genome/exome/targeted variant detection, and contaminant screening.
Brief usage overview
Download the code.
git clone --depth 1 https://github.com/igordot/sns
Generate a sample sheet based on a directory of FASTQ files.
sns/gather-fastqs <fastq_dir>
Specify the reference genome.
sns/generate-settings <genome>
Run the analysis using a specific route.
sns/run <route>
Check if the jobs are submitted and running.
squeue -u $USER
Check for problems.
grep "ERROR:" logs-sbatch/*
For more details, check the full documentation at: https://igordot.github.io/sns
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