2. Workflow Download and Setup

Clone the repository from github onto a suitable directory on your local machine or cluster with;

git clone https://github.com/ChabbyTMD/svArcher_Standalone.git

Once the SaVor repository has been cloned onto your machine. You may set up your analysis in one of two ways depending on the location of your reads.

Detail all sequence reads you intend to analyze in the .csv sample sheet located in the config/ directory, including the appropriate metadata. Refer to the next section for a description of sample sheet columns.

2.1. Description of sample sheet columns¶

2.1.1 Mandatory Fields¶

1. BioSample. This is the unique sample name for your local paired-end read data. For NCBI SRA data this will be the BioSample identifier.

2. Run. This can either be the sample name, if it was sequenced on a single lane. For multi-lane samples this column should be the sequence lane number for the R1 and R2 of the particular sequence record. For NCBI SRA data this is the run identifier listed on the samples’ SRA run selector record.

3. LibraryName: For single and multi-lane local data, this can be the name of the sample prefixed with lib_ . For multi-lane local fastq files, the library name should be the same for each sample. The following example represents a single sample, sample1, sequenced on two lanes, 1 and 2;

BioSample,Run,LibraryName,refGenome,fq1,fq2
sample1,1,lib_sample1,GCF_XXXXXXXXX.X,/path/to/sample1_lane1_1.fastq.gz,/path/to/sample1_lane1_2.fastq.gz
sample1,2,lib_sample1,GCF_XXXXXXXXX.X,/path/to/sample1_lane2_1.fastq.gz,/path/to/sample1_lane2_2.fastq.gz

1. refGenome: Provide the NCBI RefSeq accession of the reference genome for your analysis. All samples must use the same RefSeq identifier. For custom assemblies, use a consistent identifier.

2.1.2 Optional fields¶

1. refPath: For a custom assembly or reference genome e.g. masked reference, input the absolute or relative (to the repository root directory) path here. This column should be omitted if using an NCBI refSeq genome.

2. fq1 and fq2: These are the R1 and R2 absolute or relative paths for your local samples’ paired end data. Note that for samples sequenced on multiple lanes, each lanes R1 and R2 must be present in the same record.

2.2. Workflow configuration¶

In the workflow config.yaml located in the config/ directory you’ll find a number of parameters you’ll need to change specific to your analysis.

Mandatory Options:¶

1. samples : The relative or absolute path to your samples.csv file.

2. include_contigs : A simple text file with the chromosome/contig names of your reference genome/assembly. Each entry should exist on its own line.

3. use_custom_reference : Set to True if you are using a locally available reference genome. Set to False if you want your reference downloaded from NCBI’s refSeq database.

Optional options:¶

1. sort_reads: Set to True for the workflow to sort .bam files

2. mark_duplicates: Set to True for the workflow to mark duplicates

3. svBenchmark: Set to True to enable the workflows’ benchmark sub-module.

4. Path to SV benchmark base sets, deletions, duplications, inversions : These paths must be defined for your ground truth SV calls if the benchmark module is activated.