API reference

This page gives an overview of all public precellar objects, functions and methods.

Assay

Assay(path)

A Assay object.

Core functions

align(assay, aligner, *, output[, modality, ...])	Align fastq reads to the reference genome and generate unique fragments.
make_fastq(assay, *, modality, out_dir[, ...])	Generate consolidated fastq files from the sequencing specification.
make_bwa_index(fasta, genome_prefix)	Create a genome index from a fasta file.

Aligners

aligners.STAR(index_path)	The STAR aligner.
aligners.BWAMEM2(index_path)	The BWA-MEM2 aligner.

Utilities

utils.strip_barcode_from_fastq(in_fq, ...[, ...])	Remove barcode from the read names of fastq records.
utils.bam_to_fastq(input, output_dir, *[, ...])	Convert a BAM file to a FASTQ file.
utils.merge_fastq_files(input1_files, ...[, ...])	Merge multiple FASTQ files into a single output file and generate a barcode file.