API Reference

The arguments for the CLI and Python API are the same. The CLI is just a wrapper around the Python API.

CLI cmds

dreem demultiplex

dreem demultiplex [OPTIONS]

Options

--fasta <fasta>

FASTA file of all reference sequences in the project

--fastq1 <fastq1>

FASTQ files of mate 1 paired-end reads

--fastq2 <fastq2>

FASTQ files of mate 2 paired-end reads

--library <library>

Library CSV file

--barcode-start <barcode_start>

index of start of barcode

--barcode-length <barcode_length>

length of barcode

--out-dir <out_dir>

Where to output all finished files

--temp-dir <temp_dir>

Where to write all temporary files

--parallel-demultiplexing <parallel_demultiplexing>

Whether to run demultiplexing at maximum speed by submitting multithreaded grep functions

--clipped <clipped>

Designates the amount of clipped patterns to search for in the sample, will raise compution time

--mismatch-tolerence <mismatch_tolerence>

Designates the allowable amount of mismatches allowed in a string and still be considered a valid pattern find. will increase non-parallel computation at a factorial rate. use caution going above 2 mismatches. does not apply to clipped sequences.

--index-tolerance <index_tolerance>

Designates the allowable amount of distance you allow the pattern to be found in a read from the reference index

--demulti-overwrite <demulti_overwrite>

desiginates whether to overwrite the grepped fastq. should only be used if changing setting on the same sample

Python args

dreem.demultiplex.run(library: str, out_dir: str, temp_dir: str, fastq1: str, fastq2: str, fasta: str, barcode_start=0, barcode_length=0, clipped: int = 0, index_tolerance: int = 0, parallel_demultiplexing: bool = False, mismatch_tolerence: int = 0, demulti_overwrite: bool = False)