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A reference-based or genome-guided transcriptome assembly algorithm uses alignments of reads to the genome that are produced by a specialized spliced-alignment tool, such as TopHat2 (Kim et al., 2013) or GSNAP (Wu and Nacu, 2010), to identify clusters of reads that represent potential transcripts. It then builds transcript assemblies from these alignments. If paired-end reads are available, they improve the ability of the assembler to link together exons belonging to the same transcript.
(Kim et al., 2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol.
(Wu and Nacu, 2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics.
(Pertea et al., 2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol.