GUIDE-Seq An easy to use bioinformatic pipeline for the GUIDE-seq assay.
- Free software: License not yet determined.
- Documentation: https://guideseq.readthedocs.org.
- Python (2.6, 2.7, or PyPy)
- bwa alignment tool
- bedtools.
- Reference genome .fasta file (we recommend hg19)
Using this tool is simple, just create a .yaml manifest file referencing the dependencies and sample .fastq.gz file paths. Below is an example:
reference_genome: /Volumes/Media/hg38/hg38.fa
output_folder: ../tests/output
bwa: /Users/VedTopkar/code/bwa/bwa
bedtools: bedtools
undemultiplexed:
forward: ../tests/data/undemux.r1.fastq.gz
reverse: ../tests/data/undemux.r2.fastq.gz
index1: ../tests/data/undemux.i1.fastq.gz
index2: ../tests/data/undemux.i2.fastq.gz
sample_barcodes:
control: AGGCATGAGATCGC
EMX1: GACTCCTGCGATAT
Absolute paths are recommended. Be sure to point the bwa and bedtools paths directly to their respective executables.
Once you have a manifest file created, you can simply execute python guideseq.py -m PATH/TO/MANIFEST.YAML to run the entire pipeline.
You cannot run steps of the pipeline individually, though this functionality is planned for future releases.