Quick Start

Quick Start

SafeSeqS accepts the following list of run time parameters and requires (1) a set of input files in the Study Directory (2) a settings JSON file identifying study parameters in the Study Data Directory.

Run Time Parameter Descriptions

-d	Required	Directory containing the Study input files.
-r	Required	Run directory. Will be created under the Study directory.
-sf	Required	Settings file that identifies the parameters for this run. Settings file must exist in the SafeSeqs Data Directory.
-w	Optional	Number of concurrent worker sub-processes to run. Default: 1
-s	Optional	Start Stepname. Used when re-starting partially completed run. Processing will begin at the named step.
-e	Optional	End Stepname. Used when a partial run is desired. Processing will end before the named step.

Example: python -m safeseqs_controller -d C:\labName\studyName -r runName -sf SettingsTemplate.json

Required Input Files in the Study Directory

An example of each file is provided in the \example sub-directory.

1. safeseqs.json - Contains information about the study data. It identifies the FASTQ input files, the well barcode association filename, the UID length being used in the study data, and the ascii adjustment being used in the study data.

2. Study Data FASTQ Files - One or more sets of reads and barcode files - must be in the Study Directory. Both FASTQ and FASTQ.gz are supported.

3. barcodemap.txt - Tab delimited file containing mapping of samples to barcodes and primer sets.

4. primers.txt - Tab delimited file containing primers for the study.

Settings File in the Study Data Directory

A settings file must be identified at run time with the -sf argument. Parameters in the settings file control decision making during processing runs. A SettingsTemplate.json is delivered with the package. It is located in the Study Data Directory. It can be cloned and modified to create different run scenarios.

max_mismatches_for_used_reads	Required	Integer. Example 3
max_indels_for_used_reads	Required	Integer. Example 1
max_amp_per_UID_family	Required	Integer. Example 1
min_good_reads_usable_family	Required	Integer. Example 2
min_perc_good_reads_per_UID_family	Required	Integer. Example 95 = 95%
super_mut_perc_homegeneity	Required	Integer. Example 90 = 90%
default_indel_rate	Required	Float. Example .001
default_sbs_rate	Required	Float. Example .001
mark_UIDs_with_Ns_UnUsable	Optional	Valid Values: Yes or No Default: No
perform_opt_dup_removal	Optional	Valid Values: Yes or No Default: No
opt_dup_distance	Required with peform_opt_dup_removal	Integer. Example 5000
fh_limit	Required	File handle limit for system. Example 2048
load_bad_bc	Optional	Valid Values: Yes or No Default: No
load_not_used_bc	Optional	Valid Values: Yes or No Default: No

Optional Reference Data Files in the Study Data Directory

1. COSMIC.txt - Tab delimited file containing COSMIC values for known single base pair mutations. An empty file is delivered with the package.
2. dbSNP.txt - Tab delimited file containing dbSNP values for known single base pair mutations. An empty file is delivered with the package.