precellar.align#

precellar.align(seqspec, genome_index, *, modality, output_bam=None, output_fragment=None, mito_dna=['chrM', 'M'], shift_left=4, shift_right=-5, compression=None, compression_level=None, temp_dir=None, num_threads=8)#

Align fastq reads to the reference genome and generate unique fragments.

Parameters:

  • seqspec (SeqSpec | Path) – A SeqSpec object or file path to the yaml sequencing specification file, see pachterlab/seqspec.

  • genom_index (Path) – File path to the genome index. The genome index can be created by the make_genome_index function.

  • modality (str) – The modality of the sequencing data, e.g., “rna” or “atac”.

  • output_bam (Path | None) – File path to the output bam file. If None, the bam file will not be generated.

  • output_fragment (Path | None) – File path to the output fragment file. If None, the fragment file will not be generated.

  • mito_dna (list[str]) – List of mitochondrial DNA names.

  • shift_left (int) – The number of bases to shift the left end of the fragment.

  • shift_right (int) – The number of bases to shift the right end of the fragment.

  • compression (str | None) – The compression algorithm to use for the output fragment file. If None, the compression algorithm will be inferred from the file extension.

  • compression_level (int | None) – The compression level to use for the output fragment file.

  • temp_dir (Path | None) – The temporary directory to use.

  • num_threads (int) – The number of threads to use.

Returns:

A dictionary containing the QC metrics of the alignment and fragment generation.

Return type:

dict

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