Scripts¶
User Scripts¶
These are scripts that you run directly that will run the Supplemental scripts
stats_at_refpos
- runsamplesheet.sh
runsample
- graphs.sh
- consensuses.sh
miseq_sync
roche_sync
sanger_sync
ion_sync
rename_sample
make_example_config
Supplemental¶
These are scripts that you can run manually, however, they are run automatically by the User Scripts above
run_bwa_on_samplename
vcf_consensus
- gen_flagstats.sh
graphsample
graph_mapunmap
tagreads
base_caller
graph_times
trim_reads
fqstats
sample_coverage
Libraries¶
Python Scripts/Modules that you can import to do other analysis
ngs_mapper.run_bwa
ngs_mapper.reads
ngs_mapper.data
ngs_mapper.bam
ngs_mapper.alphabet
ngs_mapper.stats_at_refpos
ngs_mapper.samtools
ngs_mapper.log
Deprecated¶
Scripts that are no longer used, but kept for reference in the deprecated directory
- varcaller.py
- variants.sh
- perms.sh
- gen_consensus.sh
- setup
- install.sh