Output File Descriptions

Output Files

By default, MetaCompass produces an output folder containing an assembly file called metacompass.final.ctg.fa, the subfolder metacompass_output containing the contig file and references selected in fasta, the metacompass_sumary.tsv and metacompass_assembly_stats.tsv and the subfolder metacompass_logs with a set of output files. The --outdir

option is required, so all the output files will be placed in the specified directory.If the user specified an --keepoutput argument, the additional output folder "intermediate_files" will be created .*. If the --outdir option is used, all the output files will be placed in the specified directory.

Reference selection

MetaCompass, developed at University of Maryland, represents the first effective approach for reference-guided metagenomic assembly of low-abundance bacterial genomes that can complement and improve upon de novo metagenomic assembly methods. Given a set of reference genomes, a set of shotgun reads, and the alignment between each read and reference genome, MetaCompass applies ideas from AMOScmp building contigs from metagenomic samples. Briefly, MetaCompass selects reference genomes based on taxonomic profiles and then metagenomic reads are quickly mapped to the reference genomes. When building contigs, MetaCompass employ a greedy solution of the minimum set-covering problem to produce longer contigs.

Read mapping

Assembly

Reference-guided Assembly

De novo Assembly

Error correction