Metagenomics

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The bioinformatics applications assigned the Biological domain Metagenomics ([ ]) are tabulated below.

Definition:

Synonyms:

Query returned 40 results.

	Biological domain	Bioinformatics method	Input format	Output format
BBMap	Sequence alignment Whole genome resequencing RNA-Seq alignment SNP detection Metagenomics Phylogenetics Alternative splicing Resequencing Quality control Read binning	Read mapping Sequence alignment Sequence contamination filtering Sequence trimming RNA-Seq analysis	FASTA FASTQ SAM Scarf Paired FASTA+QUAL Interleaved Gzip	FASTA FASTQ SAM FASTA+QUAL Gzip
CANGS	Metagenomics Phylogenetics	Sequencing quality control Sequence trimming Primer removal
CatchAll	Metagenomics Population genetics
CNB MetaGenomics tools	Metagenomics Sequencing		FASTA FASTQ
DeconSeq	Genomics Transcriptomics Metagenomics	Sequence contamination filtering	FASTA FASTQ (Compressed) FASTQ (Compressed) FASTA	FASTA FASTQ
ERGO Genome Analysis and Discovery System	Transcriptomics Metagenomics Transcription factors and regulatory sites Phylogenetics Comparative genomics SNP Functional genomics Gene structure Exome analysis Genome Wide Association Studies Metabolic pathways	Sequence alignment SNP detection SNP annotation Gene expression analysis Pathway or network analysis Sequence annotation Sequence functional annotation Metabolic network modelling
FACS	Metagenomics		FASTA	FASTA
FHiTINGS	Metagenomics Comparative genomics	Sequence alignment
FragGeneScan	Genomics Metagenomics		FASTA	FASTA Tab separated
Geneious	Sequence assembly (de novo assembly) Genomics RNA-Seq Metagenomics Epigenomics Structural variation Sequence analysis Phylogenetics Population genetics	Sequence assembly Read mapping Sequence alignment Visualisation Annotation Sequence assembly validation Genome visualisation Variant calling DNA barcoding Sequence motif discovery	FASTA FASTQ SAM ELAND GenBank CSFASTA CSQUAL
Genometa	Genomics Metagenomics	Read mapping Visualisation	FASTA FASTQ	Delimited Text SAM/BAM
Gk arrays	Genomics Transcriptomics Metagenomics	Sequence assembly Read mapping Sequence error correction	FASTA FASTQ Multi-FastA
ISSAKE	Metagenomics	Sequence assembly
Krona	Metagenomics	Visualisation	Blast output MG-RAST Tab-delimited RDP PhymmBL FCP METAREP Galaxy XML	HTML
Mapsembler	Transcriptomics Metagenomics Exome capture RNA-Seq quantification Sequencing	Sequence assembly Read mapping	FASTA	FASTA XGMML (Cytoscape) Graphml (Gephi)
MEGAN	Metagenomics		SAM Blast output
Megraft	Metagenomics Sequence analysis Phylogenetics Community analysis Rarefaction	Sequence analysis	FASTA	FASTA
METAGENassist	Metagenomics Machine learning	Visualisation Statistical calculation Sequence clustering	CSV MEGAN MG-RAST Mothur QIIME STAMP Phoenix 2	CSV PDF PNG
Metagenome@Kin	Metagenomics	Species frequency estimation Statistical analysis
MetaSim	Genomics Metagenomics	Sequence assembly Mapping Modelling and simulation
Metaxa	Metagenomics Sequence analysis Phylogenetics Community analysis	Sequence analysis Hidden Markov Model	FASTA	FASTA Tab-delimited file Summary
MG-RAST	Metagenomics Phylogenetics Metabolic reconstruction	Annotation	FASTA FASTQ SFF (Compressed) FASTQ (Compressed) FASTA	FASTA BIOM
MTR	Metagenomics
Nephele	Metagenomics Microbial Ecology Microbiome	Functional analysis Taxonomic profiling Metagenomic Assembly	SFF (Compressed) FASTA 454 .fastq/.fq	Fastq.gz PDF BIOM .fasta .txt HTML report
NextGENe	Sequence assembly (de novo assembly) SNP detection Indel detection Metagenomics Exome capture		FASTA FASTQ CSFASTA/CSQUAL (ABI SOLiD) Scarf FNAQual
Phymm	Metagenomics
PRINSEQ	Genomics Transcriptomics Metagenomics	Sequence contamination filtering Sequence trimming Read pre-processing	FASTA FASTQ (Compressed) FASTQ QUAL (Compressed) FASTA	FASTA FASTQ QUAL
Proxygenes	Metagenomics	Read mapping Annotation
PyroNoise	Metagenomics Phylogenetics
RAPSearch	Metagenomics	Sequence alignment	FASTA
RDP Pyrosequencing Pipeline	Metagenomics	Sequence alignment Formatting	FASTA FASTQ
RiboPicker	Genomics Transcriptomics Metagenomics	Read pre-processing RRNA filtering	FASTA FASTQ	FASTA FASTQ
RTG	SNP detection Indel detection Metagenomics Exome and whole genome variant detection	Read mapping Sequence alignment K-mer counting Sequence contamination filtering Read depth analysis Translated nucleotide search Species frequency estimation	FASTA FASTQ SAM BAM Complete Genomics	SAM BAM BED VCF
SEED	Metagenomics	Sequence clustering	FASTQ
Sequedex	Genomics Metagenomics Phylogenetics	Sequence analysis Sequence annotation	FASTA FASTQ	FASTA FASTQ Multiple hits per read
ShoRAH	Metagenomics	Read mapping Haplotype inference	FASTA MSA
SmashCommunity	Metagenomics
Syapse	Genomics Transcriptomics DNA methylation ChIP-seq SNP detection Indel detection RNA-Seq Metagenomics DNA transcription Epigenomics Structural variation Population genetics Comparative genomics DNA-Seq Regulatory genomics	Visualisation Sequence analysis Differential expression analysis Ontology comparison Exome analysis Variant classification	VCF
TagCleaner	Transcriptomics Metagenomics	Sequence trimming	FASTA FASTQ	FASTA FASTQ
V-Xtractor	Metagenomics Sequencing	Statistical calculation	FASTA	FASTA CSV