Read mapping
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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
Category
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Bioinformatics method
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