Short read mapping
Short-read sequencing data
Short reads are small pieces of sequenced DNA obtained by → shotgun sequencing technology.
Read mapping (read alignment)
Comparing sequenced fragments (short reads) with known reference sequences.
→ Read mapping tools (Bowtie2, BWA,...)
Why do we map short reads against known sequences?
Taxonomic profiling: short reads (DNA) can be used to identifying presence and abundances of microbes in metagenomics samples, see → profiling tool MetaPhlAn 3
RNA-seq: short reads are mapped against known gene sequences to obtain the expression level of these genes in a specific mircobial environement.
Genome coverage: short reads are mapped against reference genomes to find similarities and differences of bacterial strains in a microbial sample compared to known sequenced genomes.
Strain-detection: mapping short reads against all known genomes of a species (pangenome), can be used to identify the strain-specific gene content of microbes in newly sequenced metagenomic samples, see → strain-level profiling tool PanPhlAn