RNA-Seq Alignment Tools

Biological domain Bioinformatics method Input format Output format
CLCbio Genomics Workbench Genomics
Whole Genome Resequencing
De-novo assembly
SNP discovery
InDel discovery
ChIP-Seq
RNA-Seq Alignment
MiRNA
Mapping
Assembly
Alignment
Colorspace
FASTA
FASTQ
GenBank
SAM
BAM
Illumina Bustard
ELAND
CSFASTA/CSQUAL (ABI SOLiD)
FASTA
FASTQ
GFF
GenBank
SAM
BAM
ACE
Nexus
CPTRA RNA-Seq Alignment
RNA-Seq Quantitation
Cufflinks RNA-Seq Alignment
RNA-Seq Quantitation
Differential Expression
Alternative Splicing
De novo transcriptome assembly
RNA-Seq
Assembly
Differentially expressed gene identification
statistical testing
SAM GTF
ERANGE RNA-Seq Alignment
RNA-Seq Quantitation
ChIP-Seq
Allele-specific transcription
Est2assembly RNA-Seq Alignment
Genomics
Assembly
FreClu RNA-Seq Alignment Mapping
G-Mo.R-Seq RNA-Seq Alignment
GSNAP RNA-Seq Alignment
DNA methylation
Mapping
Bisulfite mapping
HMMSplicer RNA-Seq Alignment
MapNext SNP discovery
RNA-Seq Alignment
Alignment FASTA
FASTQ
MapSplice RNA-Seq Alignment Mapping FASTA
FASTQ
SAM
BED
MIRA De-novo assembly
SNP discovery
RNA-Seq Alignment
Smith-Waterman
graph reduction
learning algorithm
Assembly
Mapping
k-mer analysis
FASTA
FASTQ
CAF
GenBank
GBFF
EXP
PHD
SCF
XML traceinfo
ACE
CAF
EXP
HTML
TXT
TCS
Myrna RNA-Seq Quantitation
RNA-Seq Alignment
Hadoop
MapReduce
Nesoni RNA-Seq Alignment
SNP discovery
Phylogenetics
Alignment SAM
FASTA
Novocraft Genomics
Whole Genome Resequencing
RNA-Seq Alignment
ChIP-Seq
MiRNA
Mapping FASTA
FASTQ
Fasta.gz
CSFASTA/CSQUAL (ABI SOLiD)
SAM
Delimited Text
TXT
OLego Genomics
RNA-Seq
RNA-Seq Alignment
Mapping
Alignment
FASTA
FASTQ
SAM
BED
PALMA RNA-Seq Alignment Alignment
PERalign RNA-Seq Alignment SAM
Qpalma RNA-Seq Alignment Alignment PSL-like
RNA-MATE RNA-Seq Alignment
RNA-Seq Quantitation
Colorspace
RSEM RNA-Seq Alignment
RNA-Seq Quantitation
Scripture RNA-Seq Alignment
SeqMan NGen Genomics
De-novo assembly
De novo transcriptome assembly
Whole Genome Resequencing
SNP discovery
InDel discovery
ChIP-Seq
RNA-Seq Alignment
Mapping
Assembly
Alignment
Paired End
FASTA
FASTQ
Scarf
SFF
SQD
ACE
PHD
ABI
AB1
GFF
CSFASTA/CSQUAL (ABI SOLiD)
SCF
TXT
GenBank
SEQ
BAM
SAM
SQD
ACE
FASTA
Sim4cc RNA-Seq Alignment
Comparative genomics
Mapping
SOCS RNA-Seq Alignment
DNA methylation
SNP discovery
Mapping
Bisulfite mapping
CSFASTA/CSQUAL (ABI SOLiD) Delimited Text
SpliceMap RNA-Seq Alignment Mapping SAM
SplitSeek RNA-Seq Alignment
Supersplat RNA-Seq Alignment Assembly
TopHat RNA-Seq Alignment FASTA
FASTQ
SAM
BED
WIG
UnoSeq RNA-Seq Alignment
De novo transcriptome assembly
USeq ChIP-Seq
RNA-Seq Alignment