dockanomics/pully repository overview

⁠pully - a utility for in silico pulldowns

pully is a utility for performing a simple in silico pulldown of paired sequence reads. A typical use case is processing a full set of paired end reads to capture those pairs that come from a certain region.

⁠Quick start

Pully is supplied with a Docker image making it easy to run:

$ docker run -it -v ${PWD}:/data dockanomics/pully:latest bash
root@3e8b0080f33f:/# cd data
root@3e8b0080f33f:/data# pully exons --regions chr22 --sample 0.01 -o few.fasta GRCh38.primary_assembly.genome.fa gencode.v35.primary_assembly.annotation.gtf
root@3e8b0080f33f:/data# pully filter -e 0.3 -c 5 -g GRCh38.primary_assembly.genome.fa -o few-filtered.fasta few.fasta
root@3e8b0080f33f:/data# pully read-pairs few-filtered.fasta x_ SRR13319535_{1,2}.fastq.gz

• The first command creates a FASTA file with exons from chromosome 22, sampled to include just 1% of transcripts using the GRCh38 (aka hg38) reference genome, and the Gencode (v35) annotation file, writing the output to few.fasta.

• The second command masks the FASTA file we created in the first step by k-merizing the sequences (with the default value of K=25) and masking low entropy k-mers (with < 0.3 bits/base), along with k-mers that occur more than 5 times across the reference genome. The masking process replaces the original bases with Ns, so they will be ignored in the subsequent pulldown of read pairs. This file is written out to few-filtered.fasta.

• The final command does the actual pulldown, using the FASTA file from the previous step as bait sequences. The bait sequences are k-merized (again with the default value of K=25), and any read pairs that share at least 1 k-mer in common with the bait sequences are written out to the files x_1.fastq and x_2.fastq. The default suffix .fastq has been used, but this can be overridden. For example, adding the option --suffix .fastq.gz will cause the reads to be compressed, though this does run more slowly, because pully runs in single thread.