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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]
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