Shortread

Shortread refers to sequencing reads produced by short-read sequencing technologies, typically 25 to 300 base pairs in length. The most widely used platforms are Illumina, Ion Torrent, and BGISEQ, which generate large volumes of data with high per-base accuracy. Reads are often obtained as paired-end sequences, meaning both ends of DNA fragments are read to provide more contextual information for alignment.

Data from short-read technologies are usually stored in FASTQ format, which combines the nucleotide sequence with per-base quality scores. Common analysis workflows include quality control and adapter trimming, alignment to a reference genome or transcriptome (examples include BWA, Bowtie2, and HISAT2), and downstream tasks such as variant calling (SNPs and indels) or expression quantification for RNA-seq. De novo genome or transcriptome assembly with short reads is feasible but more challenging than with longer reads, and is typically aided by mate-pair libraries or hybrid approaches.

Applications span whole-genome resequencing, exome sequencing, RNA sequencing, chromatin immunoprecipitation sequencing (ChIP-seq), and metagenomic surveys. Advantages of short reads include high sequencing depth, lower cost per base, and a robust ecosystem of software tools. Limitations arise from the short length, which can complicate mapping in repetitive regions, reduce the ability to detect long structural variants, and pose difficulties for assembling novel genomes. In practice, many projects combine short reads with long-read data to improve assembly quality and structural variant discovery.