All together now: high-throughput sequence mapping tool compendium

By Grant Jacobs 16/10/2012

Biologists and bioinformatics people interested in high-throughput (HTS) mapping may find this this one-page summary of all currently-available HTS mapping tools useful. The comparison table of the different features of each mapping tools will certainly beat having to dig this information out of the papers or on-line documentation. There’s also a timeline of when the methods first appeared. DNA, RNA, miRNA and bisulphite mappers are listed.

Features noted in the comparison table include:

  • The operating systems the software will run on
  • The sequencing platforms supported
  • Input and output file formats
  • Minimum and maximum read lengths
  • If mismatches, indels or gaps are supported
  • What alignments are reported if a read maps to several locations
  • If the reads are mapped locally or globally
  • Can the software be run in parallel and, if so, how
  • Are quality control measures used
  • Support for paired-end/mate-pair reads
  • In the case of RNA mapping, is splicing handled and, if so, how

The table also lists the number of citations, but I trust (and encourage) people to be swayed less by citation counts than the appropriateness of the software to their task.

This table may be a good starting point for a one of the topic pages that PLoS Computational Biology has encouraged – perhaps this might be a future direction for the authors.

Further bioinformatics-related reading on Code for life:

Forward to wikipedia – topic pages in computational biology

A bioinformatics periodic table

Choosing an algorithm — benchmarking bioinformatics

Literate and test-driven programming (in bioinformatics)

External (bioinformatics) specialists: best on the grant from the onset