Read mapping

Query returned 119 results.

	Biological domain	Bioinformatics method	Input format	Output format
AB Small Indel Tool	Indel detection Sequencing	Read mapping Sequence alignment	PAS	GFF
ABMapper	Genomics Transcriptomics	Read mapping Sequence alignment	SAM	SAM BED
AREM	ChIP-seq	Read mapping Peak calling	SAM Bowtie	BED
Array Suite (Array Studio/Server)	Genomics SNP detection Indel detection	Read mapping Gene expression profiling
BarraCUDA	Sequence analysis	Read mapping Sequence alignment	.fastq/.fq .fq.gz .bam	SAM
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
Bcbio-nextgen	Workflows	Read mapping Sequence alignment Peak calling Sequence motif recognition Genotyping Sequencing quality control Differential expression analysis Sequence trimming Filtering Genomic region matching	FASTQ	FASTQ SAM BAM BED PDF VCF
BEAP		Read mapping
BFAST	Whole genome resequencing	Read mapping Sequence alignment Genome indexing	FASTQ QSEQ CSFASTA/CSQUAL (ABI SOLiD) Compressed/uncompressed	SAM BAF
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
BioNumerics	Sequence assembly Whole genome resequencing Genotyping Sequence analysis Comparative genomics Quality control Workflows Data handling Microbial Surveillance Epidemiology	Sequence assembly Read mapping Sequence alignment Annotation Genome visualisation Variant calling Comparative genomics Workflows	FNAQual .bam (C)FAST(A/Q) Compressed fastq .ab1 And many others.
Bismark	Genomics DNA methylation Epigenomics	Read mapping Bisulfite mapping Methylation calling	FASTA FASTQ	SAM (or custom)
Bison	DNA methylation Sequencing Epigenetics	Read mapping Bisulfite mapping Methylation calling	FASTQ (Compressed) FASTQ	BAM BEDGRAPH
BLAT		Read mapping Sequence alignment	FASTA
BOAT		Read mapping
Bowtie		Read mapping Genome indexing (Burrows-Wheeler)	FASTQ	SAM
BreakSeq	Structural variation	Read mapping
BSMAP	DNA methylation	Read mapping Bisulfite mapping	FASTA FASTQ	SOAP mapping format
BWA	Mapping	Read mapping	FASTA FASTQ	SAM
BWA-SW	Mapping	Read mapping	FASTA FASTQ	SAM
CASHX	Transcriptomics	Read mapping
ChIP-Seq (application)	ChIP-seq	Read mapping Peak calling	BAM GFF BED SGA FPS	GFF BED SGA FPS
Chipster	DNA methylation ChIP-seq RNA-Seq Immunoprecipitation experiment	Read mapping Peak calling Sequence motif recognition Genome visualisation Sequencing quality control Differential expression analysis Sequence trimming Pathway or network analysis Methylation analysis	FASTQ SAM BAM BED GTF	FASTQ SAM BAM BED GTF
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
CloudAligner		Read mapping Hadoop	FASTA FASTQ	SAM
CloudBurst	SNP detection Genotyping Personalised medicine	Read mapping
CRAC	RNA-Seq alignment SNP detection Indel detection RNA-Seq quantification Alternative splicing Gene structure	Read mapping Genome indexing (Burrows-Wheeler)	(C)FAST(A/Q)	SAM (or custom)
Crossbow	SNP detection	Read mapping
Cufflinks	Transcriptomics RNA-Seq alignment RNA-Seq RNA-Seq quantification Alternative splicing	Read mapping Transcriptome assembly Differential expression analysis	SAM	GTF
ERNE	Sequence alignment Genomics DNA methylation Sequencing Epigenetics	Read mapping Bisulfite mapping	FASTQ (Compressed) FASTQ	SAM/BAM
FAAST		Read mapping	SFF
FastQ Screen	Genomics Transcriptomics	Read mapping Sequencing quality control	FASTQ	Delimited Text PNG
FreClu	RNA-Seq alignment	Read mapping
Galign	SNP detection	Read mapping
GEM library		Read mapping		SAM GFF BED WIG
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
GeneProf	ChIP-seq RNA-Seq	Read mapping Visualisation Peak calling Sequencing quality control Differential expression analysis	FASTA (Compressed) FASTQ Others (Compressed) FASTA Table with count data Tab-delimited	FASTA FASTQ BED WIG XLS TXT HTML Tab-delimited Images
Genomatix Mining Station (GMS)	ChIP-seq SNP detection RNA-Seq	Sequence assembly Read mapping SNP calling Correlation	FASTA FASTQ GenBank EMBL Solexa Solexa with Probability	FASTA SAM BAM BED GAF
GenomeMapper		Read mapping Sequence alignment
Genometa	Genomics Metagenomics	Read mapping Visualisation	FASTA FASTQ	Delimited Text SAM/BAM
GenoREAD	Sequencing Clone verification	Sequence assembly Read mapping Sequence alignment	FASTA AB1 Excel	HTML .txt JPG ZIP
Geoseq	Resequencing	Read mapping
Gk arrays	Genomics Transcriptomics Metagenomics	Sequence assembly Read mapping Sequence error correction	FASTA FASTQ Multi-FastA
GMAP		Read mapping Sequence alignment	(Compressed) FASTQ	SAM (or custom)
Gnumap		Read mapping	FASTQ
GSNAP	DNA methylation RNA-Seq alignment	Read mapping Bisulfite mapping
Hicup	Epigenomics	Read mapping	FASTQ (Compressed) FASTQ	SAM/BAM
HiPipe	Genomics	Read mapping Variant calling Workflows	Fastq.gz	VCF BAM
InGAP	SNP detection	Read mapping Sequence assembly visualisation
KARMA	DNA methylation Sequencing Epigenetics	Read mapping	FASTA FASTQ	SAM
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
LASTZ	Genomics	Read mapping Sequence alignment	FASTA Others HSX	SAM CIGAR Others MAF LAV AXT
Mapsembler	Transcriptomics Metagenomics Exome capture RNA-Seq quantification Sequencing	Sequence assembly Read mapping	FASTA	FASTA XGMML (Cytoscape) Graphml (Gephi)
MAQ	Genomics SNP detection	Read mapping	FASTA FASTQ	Maq
MAQGene	SNP detection	Read mapping Integrated solution
MethylCoder	Genomics DNA methylation Epigenomics Sequencing	Read mapping Bisulfite mapping	FASTA FASTQ	SAM TXT Binary
MicroRazerS		Read mapping	FASTA	FASTA
MIRA	Sequence assembly (de novo assembly) RNA-Seq alignment SNP detection	Sequence assembly Read mapping Local sequence alignment K-mer counting Graph reduction Learning algorithm	FASTA FASTQ GenBank PHD SCF CAF GBFF EXP XML traceinfo	ACE TXT CAF EXP HTML TCS
MirTrios	Genomics Sequence analysis De novo mutation detection	Read mapping Variant calling De novo mutation detection	VCF	BED
MOM	Genomics	Read mapping
MPscan	Genomics Transcriptomics	Read mapping	FASTA	Raw One read per line
MUMmer	Genomics Transcriptomics	Read mapping Sequence alignment	FASTA	Delta
Myrialign		Read mapping Sequence alignment
Newbler	Sequence assembly (de novo assembly)	Sequence assembly Read mapping	FASTA FASTQ SFF	FASTA BAM ACE QUAL AGP
Nexalign		Read mapping	FASTA	GFF BED TXT
Ngs backbone	Genomics SNP detection	Sequence assembly Read mapping	FASTA FASTQ	BAM GFF VCF
Ngs-pipeline	SNP detection Indel detection Epigenomics Structural variation Personalised medicine	Read mapping Sequence annotation	FASTQ BAM CSFASTA/CSQUAL (ABI SOLiD) (Compressed) FASTQ	BAM VCF
NovelSeq	Indel detection Structural variation	Sequence assembly Read mapping Variant calling	SAM DIVET	FASTA
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
Oasis	RNA	Read mapping Differential expression analysis	FASTQ (Compressed) FASTQ	XLS HTML
OLego	Genomics RNA-Seq alignment RNA-Seq	Read mapping Sequence alignment	FASTA FASTQ	SAM BED
Omixon Variant Toolkit	SNP detection Indel detection Mapping Sequence analysis Comparative genomics	Sequence assembly Read mapping Sequence alignment	FASTQ SAM CSFASTA Most others	SAM GFF VCF
PaCGeE		Read mapping	FASTQ
PALMapper		Read mapping	FASTQ	SAM BAM
PatMaN		Read mapping
PerM	Genomics SNP detection	Read mapping	FASTA FASTQ
Pindel	Indel detection Structural variation	Read mapping Split-read mapping Localised reassembly	FASTQ BAM	Gapped alignment
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
PoolHap		Read mapping Regression analysis
Proxygenes	Metagenomics	Read mapping Annotation
Pybedtools	Genomics	Read mapping	SAM BAM GFF BED VCF GTF GFF3	SAM BAM GFF BED VCF GTF GFF3
PyroMap		Read mapping
RazerS	Mapping	Read mapping Local sequence alignment	FASTA FASTQ	SAM GFF Eland AMOS
Readaligner		Read mapping
ReSeqSim	Structural variation	Read mapping Simulation
RMAP	DNA methylation	Read mapping Bisulfite mapping
RNA	Mapping	Read mapping	(Compressed) FASTQ (Compressed) FASTA	SAM BAM
RNASEQR	Alternative splicing	Read mapping
Rsubread	Next Generation Sequencing	Read mapping Read summarisation Quality assessement
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
Samscope	Genomics ChIP-seq RNA-Seq	Read mapping Visualisation	GFF BED WIG CSV GTF SAM/BAM BEDGraph	BIP
SEAL		Read mapping	QSEQ SAM PRQ
Seq2HLA	Transcriptomics Mapping	Read mapping Genetic variation analysis	FASTQ	.txt Sam Console (browser) - output
SeqBuster	Transcriptomics Regulatory RNA	Read mapping Annotation	FASTA Tab-delimited	Tab-delimited
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
SeqMap		Read mapping	FASTA	Various
SeqSaw	RNA-Seq Alternative splicing	Read mapping Sequence alignment	FASTA	SAM BED
SeqSphere+	Comparative genomics Microbial Surveillance	Sequence assembly Read mapping Variant calling	FASTA BAM GenBank ACE ABI SCF FASTA+QUAL	FASTA BAM ACE SCF
ShoRAH	Metagenomics	Read mapping Haplotype inference	FASTA MSA
SHRiMP		Read mapping
Sim4cc	RNA-Seq alignment Comparative genomics	Read mapping
Skewer	Sequence assembly RNA-Seq Small RNA Sequencing	Read mapping Adapter removal Sequence trimming Read pre-processing	(Compressed) FASTQ (Compressed) FASTA	Fasta.gz Fastq.gz Fasta/q
SNP-o-matic	SNP detection	Read mapping		SAM GFF CIGAR Pileup Others
SOAP	SNP detection	Read mapping Sequence alignment Genome indexing (Burrows-Wheeler)
SOCS	DNA methylation RNA-Seq alignment SNP detection	Read mapping Bisulfite mapping	CSFASTA/CSQUAL (ABI SOLiD)	Delimited Text
Spiral Genetics	Sequence assembly Whole genome resequencing SNP detection Mapping Sequence analysis Statistical calculation DNA-Seq Exome and whole genome variant detection Genomic assembly Quality control	Read mapping Sequence alignment File reformatting	FASTQ Fastq.gz	VCF 4.1
SpliceMap	RNA-Seq alignment	Read mapping		SAM
Stampy		Read mapping	FASTA FASTQ SAM BAM	SAM Maq
Subread	Whole genome resequencing RNA-Seq alignment Mapping Next Generation Sequencing	Read mapping	(C)FAST(A/Q)	SAM
TAPyR	Whole genome resequencing	Read mapping	FASTQ SFF	SAM BAM
TMAP		Read mapping	FASTQ SFF	BAM
VariationHunter	Structural variation	Read mapping Variant calling	DIVET
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
Vmatch		Read mapping
WHAM		Read mapping	FASTA FASTQ	SAM
ZOOM		Read mapping