fastqToFreq

Uses MinVar and bamToFreq to convert next-generation sequencing reads (fastq/fastq.gz) to frequency files (csv).

Usage

This program is intended for use via Docker only. It can be used in the following way:

docker run -v <bamFolder>:/data/ mdoering88/fastqtofreq:latest /data/

or via an interactive session

docker run -v <bamFolder>:/data/ -it --entrypoint /bin/bash mdoering88/fastqtofreq:latest

and then calling run_minvar.sh, minvar, or bamToFreq for custom processing.

Limitations

• Only single-end sequencing reads are supported (use R1 file in case of paired-end data)
• The number of reads is downsampled to speed up the computations
• Only resistant-relevant regions of HIV-1 and HCV are supported