Short read of good quality are subjected to assembly to obtain longer metagenome sequences. There are two steps involved in assembly (i) contiging and (ii) scafolding.
- contigs – contiguous stretch of sequences assembled from overlapping reads, containing paired-end reads
- scaftig – assembled contigs using paired-end information, consisting of contigs and gaps of known length
Assembly statistics
- N50 – the length of the shortest contig such that the sum of contigs of equal length or longer is at least 50% of the total length of all contigs. At least half the nucleotides in this assembly belong to contigs of size N50 length or longer. The higher N50, the more efficient the metagenome assembly
- median – a middle length in increasing length order of contigs
- mean – a mathematical average of all contig lengths
biomegen 