What is Trinity assembler?
Trinity is a tool for de novo transcriptome assembly of RNA-seq data and consists of three modules: Inchworm, Chrysalis, and Butterfly. The algorithm uses de Bruijn graphs, dynamic programming method, it can detect isoforms, handle paired-end reads, multiple insert sizes, and strandedness.
What is meant by transcriptome assembly?
Transcriptome assembly is a process of reconstructing the complete set of full-length transcripts from RNA-seq data, which often include tens of millions of short-read sequences.
How can I improve my transcriptome assembly?
Best Practices for De Novo Transcriptome Assembly with Trinity
- 1 Consult with Informatics Group staff about study design.
- 2 Examine quality metrics for sequencing reads.
- 3 Removing erroneous k-mers from Illumina paired-end reads.
- 4 Discard read pairs for which one of the reads is deemed unfixable.
How many reads for transcriptome assembly?
Experiments looking to get an in-depth view of the transcriptome, or to assemble new transcripts, may require 100–200 million reads. In these cases, researchers may need to sequence multiple samples across several high output sequencing lanes.
How long does Trinity take to run?
Trinity run-time depends on a number of factors, including the number of reads to be assembled and the complexity of the transcript graphs. The assembly from start to finish can take anywhere from ~1/2 hour to 2 hours per million reads per available CPU.
What is the transcriptome of a cell?
A transcriptome is a collection of all the gene readouts present in a cell.
Why would you expect generally shorter contigs from a transcriptome assembly than from a genome assembly?
In a genome assembly, contigs represent fragments of chromosomes or replicons. Chromosomes are much longer than transcripts. The length of the original sequence limits the sizes of contigs; therefore, the maximum length and N50, L50 values can be much larger for genomic contigs than for transcriptome assemblies.
What is a good number of reads for RNA-Seq?
The number of reads required depends upon the genome size, the number of known genes, and transcripts. Generally, we recommend 5-10 million reads per sample for small genomes (e.g. bacteria) and 20-30 million reads per sample for large genomes (e.g. human, mouse).
How does a de novo assembly work?
De novo Assembly Process Sets of overlapping or non-overlapping contigs are joined into one or more scaffolds. Sets of overlapping or non-overlapping scaffolds are joined into a single chromosome.
What is a transcriptome in genome?
A transcriptome represents that small percentage of the genetic code that is transcribed into RNA molecules — estimated to be less than 5% of the genome in humans (Frith et al., 2005). The proportion of transcribed sequences that are non-protein-coding appears to be greater in more complex organisms.
Is fewer contigs better?
A contig is defined to be correct if it aligns to the reference genome with fewer than five consecutive base mismatches at the termini and has at least 95% base similarity. By inspecting the column with the number of errors, one might conclude that lower is the number of errors better is the overall assembly quality.
What is contig assembly?
A contig is defined as a contiguous sequence assembled from a set of sequence fragments, typically by string matching and local sequence alignment. Contig assembly refers to the process of assembling many sequence fragments into one long genomic sequence or a few long contigs (Figure 3-1).
What is the purpose of transcriptome analysis?
Transcriptome analysis experiments enable researchers to characterize transcriptional activity (coding and non-coding), focus on a subset of relevant target genes and transcripts, or profile thousands of genes at once to create a global picture of cell function.