#bam #command-line-tools #convert #command-line-tool #file #command #generate #line #tools #bigwig

app bigwig2bam

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

1 unstable release

0.1.1 Feb 28, 2023


693 lines

bigwig2bam utility

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


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 --git http://gitbio.ens-lyon.fr/LBMC/Bernard/bigwig2bam.git

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

docker run -it lbmc/bigwig2bam:0.1.1 bamcalib



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
  • -h, --help Print help information
  • -V, --version Print version information


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