README.md
setup.py
pathogenseq/__init__.py
pathogenseq/bam.py
pathogenseq/fasta.py
pathogenseq/fastq.py
pathogenseq/files.py
pathogenseq/logger.py
pathogenseq/mfa.py
pathogenseq/mt_functions.py
pathogenseq/mutation_db.py
pathogenseq/mvcf.py
pathogenseq/phylo.py
pathogenseq/qc.py
pathogenseq/utils.py
pathogenseq/vcf_merge.py
pathogenseq.egg-info/PKG-INFO
pathogenseq.egg-info/SOURCES.txt
pathogenseq.egg-info/dependency_links.txt
pathogenseq.egg-info/top_level.txt
scripts/Mtb_pipeline.py
scripts/Mtb_pipeline_no_filt.py
scripts/bam2vcf.py
scripts/bam_report.py
scripts/bcf2consensus.py
scripts/bcf2dist.py
scripts/bcf2fasta.py
scripts/bcf_sample_stats.py
scripts/collate_json.py
scripts/combine_dict_list.py
scripts/cov_plt.py
scripts/csv2fasta.py
scripts/examl.py
scripts/extract_dosage.py
scripts/fasta2vcf.py
scripts/fastq_report.py
scripts/generate_run_file.py
scripts/illumina_pipeline.py
scripts/mapping.py
scripts/merge_vcfs.py
scripts/minION_pipeline.py
scripts/pathogen-profiler.py
scripts/profiler2tbprofiler.py
scripts/rename_fq.py
scripts/sambamba_depth.py
scripts/select_reference.py
scripts/splitchr.py
scripts/vcf2itol.py
scripts/venn_diagram.py