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.multiplex_fastq(input_read1, ...[, ...])

Create multiplexed FASTQ files by merging multiple FASTQ files into single output files, while generating barcodes for each read based on their file of origin.
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