File Formats

Sequence Files

Ninja-Cortex currently supports reading FASTA, FASTQ, SAM and BAM files. Also supports gzipped files. File formats are auto-detected. Commands can also read from a pipe e.g.

mccortex31 build -k 21 --sample MrSample --seq <(cat data/*.fa) mrsample.k21.ctx

It is a bad idea to use such a pipe to merge files of different formats into a single --seq argument. This also includes FASTQ files with different quality offsets.

Graph & Link Files

Cortex graph files are stored in .ctx files. Data about graph connectivity / assembly paths (known as "links") are stored in .ctp files (previously called 'path files').

Graph and link files can be loaded by specifying a subset of colours:

in.ctx:0,3-6

will load colours: 0, 3, 4, 5, 6 from graph file in.ctx. You can also specify which colour to load the first sample into:

1:in.ctx:7,9

will load colours 7 and 9 into colours 1 and 2.

Example:

mccortex31 bubbles -o out.bubbles.gz -p in.ctp:0,3-6 ... in.ctx:0,3-6

Graphviz Files

These are .dot which the dot command reads to create pretty pdf files. Download graphviz and learn more. .dot files are generated by unitigs command:

mccortex31 unitigs --graphviz graph.ctx | dot -Tpdf > graph.pdf

Alternatively, create an intermediary .dot file:

mccortex31 unitigs --graphviz --out graph.dot graph.ctx
dot -Tpdf graph.dot > graph.pdf