# Executes molecular typing on contig assemblies

## Documentation for package ‘wade’ version 0.2.5

- DESCRIPTION file.

## Help Pages

blast | Execute a given blast command
database_pipeline | Generic Profiler : SampleNo_contigs.fasta vs. arg-annot/resfinder2/CARD or VFDB
emm | emm typing pipeline from WGS assemblies
general_mlst_pipeline | Create a profile for MLST, NGMAST, or NGSTAR using blastn
labware_gono_amr | Run AMR first, then run the 23S allele counts, and then the NGSTAR-MLST analyses Then run this analysis to combine data from AMR, 23S rRNA and NG-STAR to prepare full amr profile to upload to LabWare.
master_blastr | Molecular typing pipeline for WGS assemblies

PneumoCaT_pipeline

PneumoCaT_Batch (Waffles version) : Log in to Waffles Download files from IRIDA using ngsArchiveLinker using folder structures Rename files to remove _001.fastq using: prename 's/_001.fastq/.fastq/' */*.fastq Run command line to send all samples in the "fastqs" folder : $ for sample in 'ls fastqs' ; do sbatch -c 1 -p high -mem 4G -output $sample- $ watch sq CTRL-C to exit watch.

read_vcf | Reads a .vcf file ignoring any headers, creates a data frame from the remaining lines
rna_23s | rRNA.R