Correct
Description
Correct tag to values provided in barcode allowlist.
This tag correction scheme requires one key input files aside from the reads:
- A barcode allow list (i.e. a list of all possible/allowed barcodes).
In addition, a frequency barcode list can be given. This frequency barcode list should be a TSV file of the form BARCODE COUNT. It should ideally be obtained by an orthogonal sequencing method (i.e. short reads). This frequency list will weight barcodes based on the rate at which they are known to appear in the data. The more often a barcode appears, the more likely that a read’s barcode will be corrected to it.
Command help
$ longbow correct --help
Usage: longbow correct [OPTIONS] INPUT_BAM
Correct tag to values provided in barcode allowlist.
Options:
-v, --verbosity LVL Either CRITICAL, ERROR, WARNING, INFO or
DEBUG
-p, --pbi PATH BAM .pbi index file
-t, --threads INTEGER number of threads to use (0 for all)
[default: 7]
-o, --output-bam PATH annotated bam output [default: stdout]
-m, --model TEXT The model to use for annotation. If not
specified, it will be autodetected from the
BAM header. If the given value is a pre-
configured model name, then that model will
be used. Otherwise, the given value will be
treated as a file name and Longbow will
attempt to read in the file and create a
LibraryModel from it. Longbow will assume
the contents are the configuration of a
LibraryModel as per LibraryModel.to_json().
-f, --force Force overwrite of the output files if they
exist. [default: False]
-r, --restrict-to-allowlist Restrict barcode correction possibilities to
only those on the allowlist. [default:
True]
-b, --barcode-tag TEXT The tag from which to read the uncorrected
barcode. [default: CR]
-c, --corrected-tag TEXT The tag in which to store the corrected
barcode. [default: CB]
-a, --allow-list PATH List of allowed barcodes for specified tag
(.txt, .txt.gz). [required]
--barcode-freqs PATH TSV file containing barcodes and the
frequencies associated with them in the data
(BARCODE FREQ). If not provided,
barcode freqs will be uniformly seeded by
the barcode whitelist. NOTE: If barcodes in
this freqs file are not in the allow list
and the `-r` flag is not given, it is
possibleto end up with reads that have
barcodes which where corrected to values
that are not on the allow list.
--max-hifi-dist INTEGER Maximum levenshtein distance to allow for
hifi/CCS reads during correction. [default:
2]
--max-clr-dist INTEGER Maximum levenshtein distance to allow for
CLR (ccs uncorrected) reads during
correction. [default: 3]
--ccs-corrected-rq-threshold FLOAT
Value of the `rq` tag above which reads are
considered to be CCS corrected (Hifi).
[default: 0.0]
--barcode-uncorrectable-bam PATH
File to which to write all reads with
barcodes that could not be corrected.
[default: /dev/null]
--help Show this message and exit.
Example
$ longbow correct -a 737K-august-2016.txt -m mas15v2 --barcode-freqs read_barcode_freqs.tsv tagged_array_elements.bam -o array_elements_corrected_barcodes.bam
[INFO 2022-03-01 14:08:03 correct] Invoked via: longbow correct -f -a 737K-august-2016.txt -m mas15v2 --barcode-freqs read_barcode_freqs.tsv tagged_array_elements.bam -o array_elements_corrected_barcodes.bam
[INFO 2022-03-01 14:08:03 correct] Running with 7 worker subprocess(es)
[INFO 2022-03-01 14:08:08 correct] Using mas15v2: The standard MAS-seq 15 array element model.
[INFO 2022-03-01 14:08:09 correct] Corrected tags in 570 reads of 796 total (71.61%).
[INFO 2022-03-01 14:08:09 correct] Num reads with barcodes: 796/796 (100.00%)
[INFO 2022-03-01 14:08:09 correct] Num reads without barcodes: 0/796 (0.00%)
[INFO 2022-03-01 14:08:09 correct] Done. Elapsed time: 6.09s. Overall processing rate: 130.69 reads/s.