- recipe bam2fastx
Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files
- package bam2fastx¶
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bam2fastx and update with:: mamba update bam2fastx
To create a new environment, run:
mamba create --name myenvname bam2fastx
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/bam2fastx:<tag> (see `bam2fastx/tags`_ for valid values for ``<tag>``)