Commands

To call a command:

bin/mccortex31 <command> <options>

Running a command with no options will give a help page. Available commands are:

Command	Explanation
breakpoints	use a trusted assembled genome to call large events
bubbles	find bubbles in graph which are potential variants
build	construct cortex graph from FASTA/FASTQ/BAM
calls2vcf	convert bubble/breakpoint calls to VCF
check	load and check graph (.ctx) and path (.ctp) files
clean	clean errors from a graph
contigs	assemble contigs for a sample
correct	error correct reads
coverage	print contig coverage
dist	make colour kmer distance matrix
index	index a sorted cortex graph file
inferedges	infer graph edges between kmers before calling thread
join	combine graphs, filter graph intersections
links	clean and plot link files (.ctp)
pjoin	merge path files (.ctp)
popbubbles	pop bubbles in the population graph
pview	text view of a cortex path file (.ctp)
reads	filter reads against a graph
rmsubstr	reduce set of strings to remove substrings
server	interactively query the graph
sort	sort the kmers in a graph file
subgraph	filter a subgraph using seed kmers
thread	thread reads through cleaned graph to make links
uniqkmers	generate random unique kmers
unitigs	pull out unitigs in FASTA, DOT or GFA format
vcfcov	coverage of a VCF against cortex graphs
vcfgeno	genotype a VCF after running vcfcov
view	text view of a cortex graph file (.ctx)