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?

    1. Taxonomic profiling: short reads (DNA) can be used to identifying presence and abundances of microbes in metagenomics samples, see → profiling tool MetaPhlAn 3

    2. RNA-seq: short reads are mapped against known gene sequences to obtain the expression level of these genes in a specific mircobial environement.

    3. 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.

    4. 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

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