NSCCN/pupmapper：用于将PBS作业映射到SLURM作业的转换工具

Pupmapper: A Pileup Mappability Calculator

Motivation
Installation
Basic usage
- test data set
Full usage

Motivation

The Pileup Mappability metric can be used to quickly identify regions which may be more difficult to perform variant calling with short-read WGS data. pupmapper was created to allow users to quickly convert k-mer mappability scores to pileup mappability.

The first step of the pupmapper pipeline is to calculate k-mer uniquness scores using the Genmap software. Then pupmapper will summarize the pileup mappability of each genomic position using the k-mer uniqueness of all overlapping k-mers.

How is pileup mappability calculated from individual k-mer uniqueness/mappability scores?

The Pileup mappability of a position is specifically calculated as the mean k-mer mappability of all k-mers overlapping a given position.

A pileup mappability score of 1 indicates that all k-mers overlapping with a position are unique within the genome (using the user defined parameters of uniqueness).

Simply put, Pileup mappability is useful because it gives a sense of uniquemess of all possible reads (of defined length) that could arise from given genomic position.

Useful reading for k-mer mappability and pileup mappability:

Derrien, T, (2012). Fast Computation and Applications of Genome Mappability. PLOS ONE 7(1): e30377. https://doi.org/10.1371/journal.pone.0030377

Pockrandt C, (2020) GenMap: ultra-fast computation of genome mappability, Bioinformatics, Volume 36, Issue 12, June 2020, Pages 3687–3692, https://doi.org/10.1093/bioinformatics/btaa222

Lee H, Schatz MC. (2012). Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score, Bioinformatics, Volume 28, Issue 16, August 2012, Pages 2097–2105, https://doi.org/10.1093/bioinformatics/bts330

Installation

You will need to install both the pupmapper python package and ensure that the genmap software is installed (available on your $P A T H e n v i r o n m e n t a l v a r i a b l e .) I f c o n d a i s u s e d f o r i n s t a l l a t i o n s o f t w a r e d e p e n d e n c i e s a r e i n s t a l l e d a u t o m a t i c a l l y . I f p u p m a p p e r i s i n s t a l l e d v i a ‘ p i p ‘, t h e n [g e n m a p] (h t t p s : / / g i t h u b . c o m / c p o c k r a n d t / g e n m a p) a n d [b i g t o o l s] ([h t t p s : / / g i t h u b . c o m / c p o c k r a n d t / g e n m a p] (h t t p s : / / g i t h u b . c o m / j a c k h 726 / b i g t o o l s)) n e e d t o b e i n s t a l l e d i n d e p e n d e n t l y a v a i l a b l e o n y o u r$ PATH environmental variable.).

`conda`

Installing pupmapper via conda will install both the pupmapper package and needed software dependencies (genmap and bigtools) in one command.

To install pupmapper to your current environment:

conda install -c bioconda pupmapper

To create a dedicated conda environment with pupmapper installed:

conda create -n pupmapper_env -c bioconda pupmapper

`pip`

pupmapper can be installed via pip python package manager.

pip install pupmapper

Install locally

pupmapper can be installed by cloning this repository and installing with pip.

git clone git@github.com:maxgmarin/pupmapper.git

cd pupmapper

pip install .

Basic usage

1) `pupmapper all` - Run the full pipeline starting with an input genome

pupmapper all -i Input.Genome.fasta -o output_directory/ -k 50 -e 1

The above command will first use genmap to calculate k-mer mappability scores for the input genome and then calculate pileup mappability scores.

Analyzing included test sequence

If you wish to run an pupmapper on a small test sequence (15 bp), you can run the following commands:

cd tests/data/Genmap_Ex1/

pupmapper all -i Ex1.genome.fasta -o Ex1_OutputDir -k 4 -e 0

This command will analyze the pileup mappability of the test sequence with a k-mer size of 4 bp and a max mismatch of 0 (K=4,E=0).

Full usage

pupmapper all --help
usage: pupmapper all [-h] -i IN_GENOME_FA -o OUTDIR -k KMER_LEN -e ERRORS [-g GFF] [-p PREFIX] [--save-numpy] [--save-bigwig] [--verbose]

optional arguments:
  -h, --help            show this help message and exit
  -i IN_GENOME_FA, --in_genome_fa IN_GENOME_FA
                        Input genome fasta file (.fasta)
  -o OUTDIR, --outdir OUTDIR
                        Directory for all outputs of k-mer and pileup mappability processing.
  -k KMER_LEN, --kmer_len KMER_LEN
                        k-mer length (bp) used to generate the k-mer mappability values
  -e ERRORS, --errors ERRORS
                        Number of allowed mismatches (hamming distance) in k-mer mapping step.
  -g GFF, --gff GFF     GFF formatted genome annotations for input genome (.gff) (Optional)
  -p PREFIX, --prefix PREFIX
                        File prefix for all output files generated by Pupmapper. By default, the prefix is the basename of the input genome fasta file.
  --save-numpy          If enabled, all pileup mappability scores will be output as compressed numpy arrays (.npz).
  --save-bigwig         If enabled, pileup mappability scores will be output in .bigwig format.
  --verbose             Output additional messages during processing. Useful for troubleshooting.

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