Genomics

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

Definition:

Synonyms:

Query returned 125 results.

	Biological domain	Bioinformatics method	Input format	Output format
ABMapper	Genomics Transcriptomics	Read mapping Sequence alignment	SAM	SAM BED
AnCorr	Genomics	Statistical calculation Correlation	SAM BAM GFF ELAND BED WIG TXT BEDGraph BigWig	HTML Table Graphics (png)
ANNOVAR	Genomics Genetics	Annotation Variant prioritisation
Array Suite (Array Studio/Server)	Genomics SNP detection Indel detection	Read mapping Gene expression profiling
BAMseek	Genomics Transcriptomics	Sequence alignment visualisation	SAM BAM VCF
BEDTools	Genomics	Mapping	BAM GFF BED VCF	BAM GFF BED VCF
BigBWA	Whole genome resequencing Genomics Exome capture Sequencing Resequencing Exome and whole genome variant detection Exome analysis Exome	Read mapping Sequence alignment Mapping	FASTA FASTQ BAM	SAM/BAM
BioJava	Genomics
BioPerl	Genomics
BioPHP	Genomics
Biopieces	Genomics	Sequence alignment Visualisation Sequencing quality control Sequence analysis
BioRuby	Genomics
Bismark	Genomics DNA methylation Epigenomics	Read mapping Bisulfite mapping Methylation calling	FASTA FASTQ	SAM (or custom)
BreakDancer	Genomics Indel detection Structural variation
Breakway	Whole genome resequencing Genomics Indel detection Structural variation Genetic variation	SNP calling Sequence analysis	BAM	TXT
CLCbio Genomics Workbench	Sequence assembly (de novo assembly) Whole genome resequencing Genomics Transcriptomics ChIP-seq SNP detection Indel detection RNA-Seq Regulatory RNA Mapping	Sequence assembly Sequence assembly (de-novo assembly) Read mapping Sequence alignment Ab-initio gene prediction Adapter removal Annotation Bisulfite mapping SNP calling Heat map generation Sequence assembly validation	FASTA FASTQ SAM BAM CSFASTA/CSQUAL (ABI SOLiD) ELAND GenBank Illumina Bustard	FASTA FASTQ SAM BAM GFF GenBank ACE Nexus CSV PDF XLS
CLEVER	Genomics Structural variation Copy number estimation		BAM	Tab separated
CNANorm	Genomics Copy number estimation Cancer biology	Peak calling Standardisation and normalisation	SAM BAM Delimited Text	Delimited Text
ConDeTri	Genomics RNA-Seq Sequencing	Sequence trimming	FASTQ	FASTQ
Contra	Genomics Sequencing Copy number estimation Cancer biology		BAM BED	VCF Tab-delimited
Cortex	Genomics	Sequence assembly Variant calling	FASTA FASTQ	VCF FASTA-like
CRAVAT	Genomics Genetic variation Genetics	Annotation Variant prioritisation SNP annotation Variant classification Sequence annotation	VCF TSV	TSV
DeconSeq	Genomics Transcriptomics Metagenomics	Sequence contamination filtering	FASTA FASTQ (Compressed) FASTQ (Compressed) FASTA	FASTA FASTQ
DeepTools	Genomics ChIP-seq	Visualisation Conversion Standardisation and normalisation	BedGraph BEDGraph Bed BigWig Sam Bam	BedGraph BEDGraph Bed BigWig Sam Bam
ERNE	Sequence alignment Genomics DNA methylation Sequencing Epigenetics	Read mapping Bisulfite mapping	FASTQ (Compressed) FASTQ	SAM/BAM
Est2assembly	Genomics RNA-Seq alignment	Sequence assembly
FAST: Fast Analysis of Sequences Toolbox	Genomics Sequence analysis	Sequence analysis Sequence parsing	GenBank Fasta/q Aligned Sequence Files	GenBank Fasta/q Aligned Sequence Files
FastQ Screen	Genomics Transcriptomics	Read mapping Sequencing quality control	FASTQ	Delimited Text PNG
FindPeaks 4.0 (Vancouver Short Read Package)	Genomics SNP detection	Peak calling Formatting Sequence alignment analysis	FASTA SAM BED Eland Maq Bowtie Mapview	GFF BED WIG Peaks ACE PNG Regions
Flexbar	Genomics	Adapter removal Sequence trimming DNA barcoding Quality control Read pre-processing	Fasta/q Csfasta/q	Fasta/q Csfasta/q
Forge	Sequence assembly (de novo assembly) Genomics	Sequence assembly
FragGeneScan	Genomics Metagenomics		FASTA	FASTA Tab separated
Freebayes	Genomics		BAM	VCF
Fuzzypath	Genomics	Sequence assembly Sequence assembly (de-novo assembly)	FASTQ
Galaxy	Sequence assembly Whole genome resequencing Genomics Comparative genomics Functional genomics	Sequence assembly Sequence alignment Visualisation Sequencing quality control
GeeFu	Genomics	Sequence assembly
GENALICE MAP	Genomics	Read mapping Variant calling	FASTQ	BAM VCF GAR
Genedata Expressionist	Genomics Transcriptomics DNA methylation ChIP-seq SNP detection Indel detection RNA-Seq Sequencing Laboratory information management Copy number estimation Epigenetics Gene structure	Read mapping Sequence alignment Annotation Bisulfite mapping Clustering Genome visualisation Sequencing quality control Sequence analysis Statistical calculation Gene expression analysis RNA-Seq analysis	FASTA FASTQ QSEQ SAM BAM GFF BED VCF GTF BedGraph 2bit Nib GDC And many others.
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
GenomeBrowse	Sequence assembly (de novo assembly) Sequence alignment Whole genome resequencing Genomics Sequencing Sequence analysis Genetics Exome and whole genome variant detection Exome analysis Next Generation Sequencing	Visualisation Sequence assembly visualisation Sequence alignment visualisation	BAM
GenomeJack	Genomics Personalised medicine	Visualisation	FASTA BAM GFF BED WIG VCF GTF TSV BEDGraph
Genometa	Genomics Metagenomics	Read mapping Visualisation	FASTA FASTQ	Delimited Text SAM/BAM
GenomeTools	Genomics
GenomeView	Genomics Transcriptomics Sequencing Sequence analysis Comparative genomics Quality control	Visualisation Data retrieval Genome visualisation Sequence alignment visualisation Plotting and rendering	FASTA BAM GFF BED WIG Blast output Clustalw EMBL (Compressed) FASTA GTF Multi-fasta BEDGraph	Gff3 Embl
GenomicTools	Genomics ChIP-seq RNA-Seq	Peak calling Heat map generation Genome comparison	GFF BED SAM/BAM	SAM GFF BED
GenVision	Genomics	Visualisation
GigaBayes	Genomics SNP detection	SNP calling
Gk arrays	Genomics Transcriptomics Metagenomics	Sequence assembly Read mapping Sequence error correction	FASTA FASTQ Multi-FastA
Golden Helix	Genomics SNP detection Epigenomics Sequencing Copy number estimation Data handling	Annotation Genome visualisation Sequencing quality control Sequence contamination filtering Variant calling Statistical calculation Collapsing methods Variant classification
Gowinda	Genomics Sequencing Population genetics Population Genomics	Ontology comparison Functional enrichment Genome-wide association study	VCF Pileup GTF
GPS	Genomics ChIP-seq Epigenomics Transcription factors and regulatory sites	Peak calling	ELAND BED Bowtie SAM/BAM
GRIDSS	Genomics Structural variation Genetic variation analysis	Sequence assembly Split-read mapping Read alignment Assembly Whole genome breakend assembly	SAM BAM CRAM	BAM VCF BEDPE
HeliSphere	Whole genome resequencing Genomics SNP detection RNA-Seq	Mapping	SMS	FASTA FASTQ SAM BAM BED WIG
HiPipe	Genomics	Read mapping Variant calling Workflows	Fastq.gz	VCF BAM
IGV	Genomics	Visualisation	FASTA SAM BAM GFF BED PSL GTF GOBY CN GCT
Illuminate	Genomics	Sequencing quality control	.bin and .xml files from rundata directory	Python data structures Some textual output
Ingenuity Variant Analysis	Whole genome resequencing Genomics SNPs Exome	Variant classification
Integrated Genome Browser	Genomics	Visualisation	BAM GFF BED PSL	Various image file formats
IOmics	Genomics Transcriptomics ChIP-seq RNA-Seq Regulatory RNA Exome capture Epigenomics	Sequence assembly Sequence alignment Ab-initio gene prediction Variant calling MiRNA analysis Exome analysis
Knime4Bio	Genomics Transcription factors and regulatory sites Gene regulation	Data retrieval	Delimited Text VCF	Various
Lab7	Genomics Laboratory information management	Workflows
Lasergene	Sequence assembly (de novo assembly) Genomics SNP detection Indel detection Mapping Transcription factors and regulatory sites Sequence analysis Phylogenetics Protein structure analysis	Sequence assembly Read mapping Sequence alignment Peak calling Annotation Sequence analysis Scaffolding Sequence alignment analysis Chromatogram visualisation PCR primer design
LAST	Genomics Comparative genomics	Sequence alignment	FASTA
LASTZ	Genomics	Read mapping Sequence alignment	FASTA Others HSX	SAM CIGAR Others MAF LAV AXT
LSKB, Life Science Knowledge Bank	Genomics	Annotation SNP calling Sequence analysis Differential expression analysis Pathway or network analysis Classification Analysis pipeline Functional analysis
MAQ	Genomics SNP detection	Read mapping	FASTA FASTQ	Maq
Mason	Genomics	Sequence assembly Mapping Modelling and simulation	FASTA	FASTA FASTQ SAM
Mauve	Genomics Transcriptomics	Visualisation Sequence assembly validation Sequence alignment comparison	FASTA GenBank Multi-FastA	XMFA
MAXIMUS	Genomics	Sequence assembly
MetaSim	Genomics Metagenomics	Sequence assembly Mapping Modelling and simulation
MethylCoder	Genomics DNA methylation Epigenomics Sequencing	Read mapping Bisulfite mapping	FASTA FASTQ	SAM TXT Binary
MirTrios	Genomics Sequence analysis De novo mutation detection	Read mapping Variant calling De novo mutation detection	VCF	BED
MochiView	Genomics ChIP-seq RNA-Seq ChIP-on-chip Sequence motifs	Genome visualisation Sequence motif comparison	FASTA GFF BED WIG Custom MEME Bioprospector Custom Motif format	Varied
MoDIL	Genomics Indel detection
MOM	Genomics	Read mapping
MPscan	Genomics Transcriptomics	Read mapping	FASTA	Raw One read per line
MrCaNaVaR	Genomics Personalised medicine Copy number estimation	Read depth analysis	SAM	BED (copy numbers)
MrFAST	Genomics Read alignment	Read alignment	FASTA FASTQ	SAM DIVET
MrsFAST	Genomics	Mapping Read alignment	FASTA FASTQ	SAM DIVET
MUMmer	Genomics Transcriptomics	Read mapping Sequence alignment	FASTA	Delta
MUMmerGPU	Genomics Transcriptomics	Sequence alignment
MuMRescueLite	Genomics ChIP-seq	Mapping
Ngs backbone	Genomics SNP detection	Sequence assembly Read mapping	FASTA FASTQ	BAM GFF VCF
NGSUtils	Genomics Transcriptomics	Formatting Sequencing quality control Sequence contamination filtering Variant calling Read pre-processing	BAM BED (Compressed) FASTQ GTF
NGSView	Genomics	Sequence assembly visualisation
Novocraft	Whole genome resequencing Genomics ChIP-seq RNA-Seq alignment Regulatory RNA	Read mapping	FASTA FASTQ CSFASTA/CSQUAL (ABI SOLiD) Fasta.gz	SAM TXT Delimited Text
ODIN	Genomics Regulatory genomics	Peak calling	BAM BED	BED BigWig
OLego	Genomics RNA-Seq alignment RNA-Seq	Read mapping Sequence alignment	FASTA FASTQ	SAM BED
PerM	Genomics SNP detection	Read mapping	FASTA FASTQ
Pipeline Pilot	Sequence assembly (de novo assembly) Whole genome resequencing Genomics ChIP-seq SNP detection RNA-Seq Sequence analysis Gene expression analysis Next Generation Sequencing	Read mapping Sequence alignment Sequence analysis Variant calling Comparative genomics Gene expression analysis	Velvet MUMmer Bowtie CisGenome MACS TopHat SAMtools BWA GATK Cufflinks Tablet BLAST MUSCLE BreakDancerMax CNV-seq FASTQC Integrative Genomics Viewer Mapreads MIRA3 SnpEff Tabix Artemis BioJava BioPerl ClustalW EMBOSS HMMER Jalview Primer3 PROSITE Sim4	Circos GBrowse2
PoPoolation2	Genomics Population genetics
PRINSEQ	Genomics Transcriptomics Metagenomics	Sequence contamination filtering Sequence trimming Read pre-processing	FASTA FASTQ (Compressed) FASTQ QUAL (Compressed) FASTA	FASTA FASTQ QUAL
Pybedtools	Genomics	Read mapping	SAM BAM GFF BED VCF GTF GFF3	SAM BAM GFF BED VCF GTF GFF3
RAST	Genomics Phylogenetics	Genomics Annotation
Reptile	Genomics	Sequencing quality control
RiboPicker	Genomics Transcriptomics Metagenomics	Read pre-processing RRNA filtering	FASTA FASTQ	FASTA FASTQ
Samscope	Genomics ChIP-seq RNA-Seq	Read mapping Visualisation	GFF BED WIG CSV GTF SAM/BAM BEDGraph	BIP
Savant Genome Browser	Genomics	Visualisation Sequence alignment visualisation	FASTA SAM BAM GFF BED WIG Tab-delimited
SCALCE	Genomics	File reformatting	FASTQ	Scalcer Scalceq Scalcen
Segemehl	Genomics	Mapping	FASTA	Plain text mapping list Multiple hits per read (if found) Unknown standard (if any)
SeqAn	Genomics Sequence analysis Phylogenetics		FASTA FASTQ SAM GFF	FASTA FASTQ SAM GFF
SeqGSEA	Genomics RNA-Seq Biomedical Sciences	Statistical calculation Functional enrichment Functional analysis	SAM BAM	Tab separated
SeqMan NGen	Sequence assembly (de-novo assembly) Sequence assembly (de novo assembly) Whole genome resequencing Genomics ChIP-seq RNA-Seq alignment SNP detection Indel detection Transcriptome assembly	Sequence assembly Read mapping Sequence alignment	FASTA FASTQ CSFASTA/CSQUAL (ABI SOLiD) GFF GenBank ACE Scarf SFF SQD PHD ABI AB1 SCF TXT SEQ	FASTA SAM BAM ACE SQD
SeqMonk	Genomics Epigenomics	Visualisation Sequence assembly visualisation Sequence alignment visualisation Statistical calculation	SAM BAM GFF BED Eland Maq Delimited Text Bowtie Bismark	Delimited Text PNG SVG
SeqPrep	Sequence assembly (de novo assembly) Genomics		FASTQ	FASTQ
Sequedex	Genomics Metagenomics Phylogenetics	Sequence analysis Sequence annotation	FASTA FASTQ	FASTA FASTQ Multiple hits per read
SequenceVariantAnalyzer	Genomics Personalised medicine Sequence analysis Genetic variation	Annotation SNP calling Genome visualisation	SAMtools HMMCNV	Sva
Sherman	Genomics DNA methylation Sequencing Epigenetics	Modelling and simulation		FASTQ CSFASTA/CSQUAL (ABI SOLiD)
Sibelia	Genomics	Variant calling	FASTA
SimSeq	Genomics	Modelling and simulation	FASTA	SAM
SplicingViewer	Genomics RNA-Seq	Mapping	SAM/BAM	GFF Tab
SPP	Genomics ChIP-seq	Peak calling	ELAND MAQ Bowtie Arachne binary
SSPACE	Genomics	Scaffolding	FASTA FASTQ	FASTA
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
Tablet	Genomics Genotyping Comparative genomics	Sequence assembly visualisation	FASTA FASTQ SAM BAM MAQ SOAP ACE AFG VCF GTF GFF3	PNG
Tripal	Genomics Genetics	Visualisation	FASTA GFF3 Chado DB
UGENE	Genomics Sequence analysis Phylogenetics Protein structure analysis	Sequence parsing	FASTA FASTQ SAM GFF Fasta.gz GenBank ACE AB1 Phylip Clustalw EMBL Newick Stockholm MSF	FASTA SAM Fasta.gz GenBank ACE Clustalw Newick Stockholm
Variation toolkit	Genomics SNP Exome and whole genome variant detection	SNP annotation	Delimited Text VCF	FASTA Delimited Text VCF Postscript
VARiD	Genomics SNP detection Indel detection	Statistical calculation	SAM
Vcflib	Genomics		VCF	VCF
VIP	Genomics SNP	SNP detection Mapping SNP annotation	Fasta	Output to local database
ViralFusionSeq	Sequence assembly (de novo assembly) Genomics Mapping Gene structure	Sequence assembly Read mapping Sequence alignment Read pre-processing	FASTQ (Compressed) FASTQ Single-end and Paired end	FASTA Custom .fasta
VirusSeq	Genomics Mapping	Read mapping	FASTQ
WebApollo	Genomics Sequence annotation Sequence functional annotation	Annotation	BAM GFF3 BigWig	BED GFF3
ZORRO	Genomics	Sequence assembly	FASTA	FASTA