Converts bam or cram files to fastq format and does quality control.
This pipeline converts (un)mapped
.bam files into
Initially, it auto-detects, whether the input file contains single-end or paired-end reads. Following this step, the reads are sorted using
samtools collate and extracted with
samtools fastq. Furthermore, for mapped bam files it is possible to only convert reads mapping to a specific region or chromosome. The obtained FastQ files can then be used to further process with other pipelines.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.
iii. Download the pipeline and test it on a minimal dataset with a single command
iv. Start running your own analysis!
See usage docs for all of the available options when running the pipeline.
The qbic-pipelines/bamtofastq pipeline comes with documentation about the pipeline, found in the
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
qbic-pipelines/bamtofastq was originally written by Friederike Hanssen.
The individual steps of this pipeline are based of on the following tutorials and resources:
- Extracting paired FASTQ read data from a BAM mapping file
- Check if BAM is derived from pair-end or single-end reads
Contributions and Support
If you would like to contribute to this pipeline, please see the contributing guidelines.
For further information or help, don’t hesitate to get in touch by opening an issue.
If you use qbic-pipelines/bamtofastq for your analysis, please cite it using the following doi: 10.5281/zenodo.4022137