Table 1.

Summary of strategies used for generating metatranscriptomic assemblies.

	Trans-ABySS	Trinity	Oases	IDBA-tran	Rockhopper
Version	1.5.2	r20131110	0.2.0	1.1.0	2.0
Assembly method	De novo assembly using de Bruijn graph
k-mer size (min, max, step)	61, 101, 4	25	61, 101, 4	61, 101, 4	25
Minimum contig size	200 bp	200 bp	200 bp	300 bp	200 bp
Option “strand-specific” specified?	Yes	Yes	Yes	Not available	Yes
No. of intermediate assemblies generated	11	1	11	11	1
Merging of assemblies	Pairs of assemblies with adjacent k values were reciprocally compared to find representative contigs. Representative contigs were the longest parent contig to which the shorter contigs had an exact match. The merging step was reiterated.	No applicable	Contigs in the 11 assemblies were used as input for assembly in Velvet. The k-mer (or KMERGE) size of 27, options “-long,” “-conserveLong,” and “-read_trkg” were used. Identical graphs across the 11 assemblies were removed.	Assemblies were generated reiteratively with the contigs generated in the previous assembly being used to generate k-mers for the next assembly.	No applicable