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: