Sequencing

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

Definition:

Synonyms:

Query returned 41 results.

	Biological domain	Bioinformatics method	Input format	Output format
4peaks	Sequencing	Sequence analysis
AB Large Indel Tool	Indel detection Sequencing	Mapping	CMAP	GFF
AB Small Indel Tool	Indel detection Sequencing	Read mapping Sequence alignment	PAS	GFF
Anno-J	Sequencing	Visualisation
Avadis NGS	ChIP-seq RNA-Seq Sequencing DNA-Seq Small RNA-Seq RNA Methyl-Seq MeDIP-Seq Pathway or network analysis	Sequence alignment Visualisation Sequencing quality control Sequence analysis Analysis Biological interpretation	FASTA FASTQ SAM BAM ELAND BED Unaligned BAM	HTML VCF Tab-delimited Tab separated .txt TSV
BayesCall	Sequencing	Base-calling
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
BiQ Analyzer HT	DNA methylation Sequencing Epigenetics
Bis-SNP	DNA methylation SNP detection Sequencing Genotyping Epigenetics	Bisulfite mapping SNP calling Methylation calling	BAM	BED WIG VCF BEDGRAPH
Bison	DNA methylation Sequencing Epigenetics	Read mapping Bisulfite mapping Methylation calling	FASTQ (Compressed) FASTQ	BAM BEDGRAPH
BSSim	DNA methylation Sequencing Epigenetics	Modelling and simulation	FASTA	FASTQ SAM Ref
CNB MetaGenomics tools	Metagenomics Sequencing		FASTA FASTQ
ConDeTri	Genomics RNA-Seq Sequencing	Sequence trimming	FASTQ	FASTQ
Contra	Genomics Sequencing Copy number estimation Cancer biology		BAM BED	VCF Tab-delimited
DiscoSnp	Sequence assembly (de novo assembly) Sequencing Genotyping Comparative genomics High-throughput sequencing Population Genomics	Sequence assembly (de-novo assembly) Read depth analysis	FASTQ Fasta Compressed fasta Compressed fastq	Fasta
ERNE	Sequence alignment Genomics DNA methylation Sequencing Epigenetics	Read mapping Bisulfite mapping	FASTQ (Compressed) FASTQ	SAM/BAM
Figaro	Sequencing	K-mer counting	FASTA Trace Archive	FASTA QUAL AFG Clipping coordinates (CLR)
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.
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
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
GenoREAD	Sequencing Clone verification	Sequence assembly Read mapping Sequence alignment	FASTA AB1 Excel	HTML .txt JPG ZIP
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
Ibis	Sequencing	Base-calling	Intensity files (int.txt.gz Int.txt.p.gz Cif) and Cluster coordinates (idx Pos)	FASTQ
KARMA	DNA methylation Sequencing Epigenetics	Read mapping	FASTA FASTQ	SAM
LobSTR	Sequencing	Repeat sequence organisation analysis	FASTA FASTQ BAM	BAM Custom
MapDamage	Sequencing DNA	Sequencing quality control Statistical calculation	SAM BAM
Mapsembler	Transcriptomics Metagenomics Exome capture RNA-Seq quantification Sequencing	Sequence assembly Read mapping	FASTA	FASTA XGMML (Cytoscape) Graphml (Gephi)
Methpipe	DNA methylation Sequencing Epigenetics	Bisulfite mapping	FASTQ SAM/BAM
MethylCoder	Genomics DNA methylation Epigenomics Sequencing	Read mapping Bisulfite mapping	FASTA FASTQ	SAM TXT Binary
NCBI Genome Workbench	Sequencing Sequence analysis Sequence annotation Next Generation Sequencing	Visualisation Genome visualisation
PeakTrace	Sequencing	Base-calling	.ab1 .abi .abd	.ab1 .scf .seq .phd.1
Rolexa	Sequencing	Base-calling
RUbioSeq	DNA methylation Sequencing Copy number estimation Epigenetics Exome analysis	Variant calling	FASTQ	VCF
Sherman	Genomics DNA methylation Sequencing Epigenetics	Modelling and simulation		FASTQ CSFASTA/CSQUAL (ABI SOLiD)
Subjunc	RNA-Seq alignment Mapping Sequencing RNA splicing	Read alignment	FASTQ
SwDMR	DNA methylation Sequencing Epigenetics	Methylation calling	Others	WIG PDF SVG Regions
Tally	Sequencing	Sequence contamination filtering Read pre-processing Sequence redundancy removal	(Compressed) FASTQ (Compressed) FASTA Table with count data Tab-delimited Customizable	Fasta.gz Custom Tab-delimited Fasta/q
Tracembler	Sequencing	Sequence assembly
V-Xtractor	Metagenomics Sequencing	Statistical calculation	FASTA	FASTA CSV
ZINBA	ChIP-seq Sequencing		BED