#bam #file #genome #convert #bigwig #command-line #fasta

app bigwig2bam

A command line tools to convert bigwig file into single-end bam file

4 releases

0.1.4 Feb 5, 2024
0.1.3 Dec 18, 2023
0.1.2 Dec 6, 2023
0.1.1 Feb 28, 2023

#93 in Science

40 downloads per month

AGPL-3.0-or-later

40KB
762 lines

bigwig2bam utility

bigwig2bam is a small rust program to convert bigwig file to bam file

Installation

You need cargo installed

  • curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
  • sudo apt install cargo
  • sudo pacman -S rust
  • brew install rust

Then run the following command:

cargo install bigwig2bam --version 0.1.1

You can also use the lbmc/bigwig2bam:0.1.1 Docker image

docker run -it lbmc/bigwig2bam:0.1.1 bigwig2bam

Usage

Example

bamcalib \
  --bigwig IP_11.bigwig \
  --fasta genome.fasta \
  --bam IP_11.bam \
  --read_length 150

The bigwig2bam expect the following parameters:

  • --bigwig <bigwig_file> bigwig file to convert
  • --fasta <fasta_file> fasta genome from which to generate the read sequences
  • --output-bam <bam_file> output bam file (sorted)

Optional Arguments

  • -c, --cal-prefix <cal_prefix> calibration prefix added to the chromosome name of the calibration genome (default: calib_)
  • --read_length <value> size of the reads to generate
  • --avoid-empty-bam add +1 to the density to avoid empty bams
  • -h, --help Print help information
  • -V, --version Print version information

Dependencies

~22–34MB
~501K SLoC