CAG creation (GUI)

Contig adjacency graphs can be created by selecting “Create CAG” from the “File” menu

Contig file – FASTA file of contigs or scaffolds

Read file – Interleaved fastq file - read1_left, read1_right, read2_left... orientated as such --> <--

Get overlapping edges – Find edges by looking for overlapping edges (Requires BLAST)

Minimum overlap length – Minimum overlap to consider two contigs adjacent

Maximum mismatches in overlap – Maximum number of mistmatches allowed in that overlap

Get de bruijn edges – Find edges using a De Bruijn graph

Kmer size – kmer size used to construct De Bruijn graph

Max. distance: Distance (in bp) to search in the De Bruijn graph for an adjacent contig (this value + kmer size)

Auto detect cutoffs – Automatically detect coverage cutoff and median unique kmer frequency

kmer cutoff – kmers with a frequency less than this value will not be traversed

kmer average – median unique kmer frequency: all kmers with a frequency greater than this value will be traversed

Get edges using paired reads: Find edges by mapping paired-end reads (Bowtie-2 required)

Max. insert size: Only reads with an insert size smaller than this will be counted

Minimum read length: Only reads that have at least this value of bases mapping will be counted

Min. reads for edge: Minimum mapping reads to create an edge between two contigs