In the age of fast development of tools for next-generation sequencing, the bioinformatics tools for processing of a large amount of data have an exceptional meaning. In the last few years, the RNA-seq method has established itself as a useful method in transcriptomics. Its output are short reads, which ha to be assembled in a possible transcripts. For transcript assembly two approaches are available. The first one is genome-guided assembly of transcripts. Using this approach the RNA-seq reads are aligned to the reference genome. The second approach is de-novo transcript assembly where we do not have the reference sequence, so the transcript is built from scratch. Both approaches have pros and cons. Genome guided assembly is appropriate for model organisms since their genomes are well annotated and used as a reference. De-novo approach is more appropriate for non-model organisms where genome sequence is not available. The purpose of this work is the presentation of both approaches, review of some commonly used tools and their comparison.
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