Reference-based assembly is a genome assembly approach that relies on a previously sequenced and annotated reference genome as a scaffold for the assembly of new sequencing data. In reference-based assembly, sequencing reads are aligned to the reference genome, and the aligned reads are used to generate a consensus sequence for the new genome assembly.
Here are some commonly used tools for reference-based assembly:
BWA: This is a widely used read aligner that can align short-read sequencing data to a reference genome. BWA is known for its accuracy and speed and is often used as the first step in the reference-based assembly process.
Bowtie2: This is another popular read aligner that can align short-read sequencing data to a reference genome. Bowtie2 is optimized for speed and accuracy and is also commonly used in the reference-based assembly process.
SAMtools: This is a suite of tools for working with SAM/BAM format files generated by read aligners such as BWA and Bowtie2. SAMtools can be used to filter, sort, and manipulate read alignments, and can be used to generate consensus sequences for the reference-based assembly.
Genome Analysis Toolkit (GATK): GATK is a software package for variant discovery and genotyping from high-throughput sequencing data. GATK can be used to improve the accuracy of the reference-based assembly by correcting sequencing errors and identifying variants.
HISAT2: This is a read aligner that is specifically designed for spliced alignment of RNA-seq data to a reference genome. HISAT2 is known for its speed and accuracy and is commonly used in gene expression and transcriptome analysis.
TopHat: This is a software tool for aligning RNA-seq reads to a reference genome, and for identifying novel splice junctions and gene fusions. TopHat is optimized for sensitivity and accuracy and can be used to improve the accuracy of the reference-based assembly of transcriptomes.
Pilon: This is a software tool for polishing genome assemblies generated by both reference-based and de novo assembly methods. Pilon can be used to correct errors and fill gaps in the assembly using high-quality short-read sequencing data aligned to the assembly.
STAR: This is a highly sensitive and accurate RNA-seq read aligner that can align reads to both genomes and transcriptomes. STAR can be used for both reference-based and de novo transcriptome assembly.
RAxML: This is a software package for maximum likelihood-based phylogenetic analysis. RAxML can be used to construct phylogenetic trees using reference genomes and assembled genomes from multiple species.
These tools are just a few examples of the many software programs available for reference-based assembly. The choice of tool will depend on the specific characteristics of the reference genome and the sequencing data being analyzed.