Table 1 List of bioinformatics tools and resources currently incorporated within A-GAME
From: A-GAME: improving the assembly of pooled functional metagenomics sequence data
Quality Trimming | |
|---|---|
Tool | Reference |
FastQC | [30] |
Pear | [31] |
Flash | [32] |
Trimmomatic | [33] |
FastX | [34] |
Assembly | |
Megahit | [35] |
SPAdes | [36] |
Abyss | [37] |
Velvet | [38] |
Meta-Velvet | [39] |
Meta-SPAdes | [40] |
Gene prediction | |
Glimmer | [41] |
Augustus | [42] |
Prokka (Prodigal) | [43] |
Metagenemark | [28] |
Functional annotation | |
Interpro | [44] |
PFAM | [45] |
Blast + suite | [46] |
Short read mapping | |
Bowtie2 | [47] |
bwa | [48] |
Scaffolding | |
SSpace | [23] |
Sopra | [49] |