Type-Pacbio

An assembler: is a type of software or tool used in the process of genome or transcriptome assembly. Genome or transcriptome assembly involves reconstructing longer, more complete sequences from short DNA or RNA sequencing reads. Assemblers take these short reads as input and use various algorithms to piece them together into longer sequences, ultimately producing a more comprehensive picture of the genome or transcriptome being studied.

There are different approaches and algorithms used by assemblers, including de Bruijn graph, overlap-layout-consensus (OLC), and hybrid assembly methods. Each assembler may have its own advantages and limitations, and the choice of assembler depends on factors such as the type of data, the research objectives, and specific project requirements.

⬝Upload samples ➔ save ( create sample failed)➔ Edit (change name, change project) and submit ➔ assembler ➔ new run➔assembler reads with (choose 1 of 4): Unicycler, Hifiasm Meta, Canu, Flye

1. Unicycler: is a bioinformatics tool used for genome assembly, particularly for bacterial and viral genomes. It's designed to automatically generate complete genomes from short-read sequencing data, including both chromosomal and plasmid-encoded genes. Unicycler utilizes a hybrid assembly approach, combining elements of both de Bruijn graph and overlap-layout-consensus (OLC) methods to handle sequencing data and produce highly contiguous genome sequences. The tool automatically adjusts and assembles reads, including repetitive regions and complex genomic structures.

   ⬝Assemble reads with Unicycler

   ⬝Type:

   • Long reads ➝ long reads library (choose file)
   • Short reads ➝ Unpaired short reads library ➝ Paired end short reads library
   • Hybrid ➝ Long reads library ➝ Unpaired short reads library ➝ Paired end short reads library

2. Hifiasm Meta ➔ Sample

3. Canu ➔ Genome size ➔ Sample

4. Flye ➔Sample