contigs.fasta is a generic file name, indicating a file that contains a set of finalized contigs in fasta format. The function of contigs.fasta depends on its location; it may appear in the following directories:
- PRE/vector, PRE/e_coli, PRE/e_coli_transposons: Required input file containing a broad selection of sequences from either the bacterial host mitochondrial DNA or from sequencing vectors. Be sure to add your sequencing vectors to this file if they are not already in it.
- DATA: Optional input file containing a finished sequence, in the form of known contigs or BACs. Arachne uses this file, if it exists, in generating the output file assembly.ps: it evaluates the quality of the draft assembly by aligning it with the sequenced contigs. Note that Arachne does NOT use this file at any point during the assembly process; it is used solely for output purposes.