gcMeta: integrated microbiome research platform

Assembly

ToolsKey wordsLinks
SOAPdenovo2 large genome assembly   
SPAdes genome, metagenome assembly   
MetaVelvet metagenome assembly   
ALLPATH-LG genome assembly   
Meta-IDBA metagenome assembly   
MEGAHIT metagenome assembly   
RayMeta metagenome assembly   
CANU long reads assembly (TGS)   
CAP3 extension   
SSPACE extension   
OPERA scaffolding   
QUAST assembly quality validation   
REAPR assembly quality validation   
CheckM assembly completeness validation   
BUSCO assembly completeness validation   
cufflinks transcriptome assembly (RNA)   
StringTie transcriptome assembly (RNA)   
Cuffdiff differential expression (RNA)   
Sailfish de novo differential expression (RNA)  
Kallisto de novo differential expression (RNA)  
DESeq2 differential expression (RNA)   
Ballgown differential expression (RNA)   
Trinity de novo transcriptome assembly (RNA)   
Oases de novo transcriptome assembly (RNA)   
SOAPdenovo-Transde novo transcriptome assembly (RNA)