Barcode Splitter

A utility to split multiple sequence files using multiple sets of barcodes.

Installation

Install Barcode Splitter:
```
pip install barcode_splitter
```

barcode_splitter

Split multiple fastq files by matching barcodes in one or more of the sequence files. Barcodes in the tab-delimited barcodes.txt file are matched against the beginning (or end) of the specified index read(s). By default, barcodes must match exactly, but --mistmatches can be set higher if desired. Compressed input is read (from all files) if the first input file name ends in .gz. Reading of compressed input can be forced with the gzipin option.

Examples

Split an Illumina paired-end run where the index read are in the second read file (read 2), the forward read is the first read file (read 1), and the reverse reads are in the third read file (read 3):

barcode_splitter --bcfile barcodes.txt read1.fastq read2_index.fastq read3.fastq --idxread 2 --suffix .fastq

UTF-8

Sample names containing UTF-8 characters are allowed, however, outputting those characters to STDOUT and piping to a file can be problematic. Ensure python uses the proper encoding for STDOUT by setting PYTHONIOENCODING='utf-8'.:

PYTHONIOENCODING='utf-8' barcode_splitter --bcfile barcodes_utf8.txt read1.fastq read2_index.fastq read3.fastq --idxread 2 --suffix .fastq

Citation

Please use the following BibTeX entry:

@misc{leach_bcs_2019,
    address = {Princeton, {NJ}, {USA}},
    title = {Barcode Splitter, version 0.18.5 [Software]},
    url = {https://bitbucket.org/princeton_genomics/barcode_splitter},
    author = {Leach, Robert and
              Parsons, Lance},
    year = {2019}
}

Metadata

Release files for barcode-splitter 0.18.6

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Built distribution (wheel)

Table of built distributions (wheels) for barcode-splitter 0.18.6
File	Interpreter	ABI	Platform	Reset
barcode_splitter-0.18.6-py2.py3-none-any.whl 15.0 kB Jul 22, 2019	Python 3, Python 2	none	any	Details

Release files / barcode_splitter-0.18.6-py2.py3-none-any.whl

Download URL	barcode_splitter-0.18.6-py2.py3-none-any.whl
Size	15.0 kB
Tags	Python 2 Python 3
SHA-256 checksum How to use checksums	`4d573cf5bcf0c9c5d46b6ba1704ad0d5408b33adeeacddc42d7a7b928610911d`
BLAKE2b-256 checksum How to use checksums	`88eb393381d43fe2a47b6b2d798f553754b96071988accbdebb4c622fd369ee3`
Upload date	Jul 22, 2019
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/1.13.0 pkginfo/1.5.0.1 requests/2.19.1 setuptools/40.0.0 requests-toolbelt/0.8.0 tqdm/4.31.1 CPython/2.7.15`