R2R - From Reads to Results
"It doesn't have to be so complicated"

R2R is a simple to use package for very sensitive analysis of short read sequence data obtained by NextGen sequencing techniques. R2R was developed in conjunction with data obtained on the Illumina GA platforms. R2R is written in simple Perl script and runs equally well under MS Windows, Mac OS and Linux/Unix operative systems.

Current version: Version 0.950


What is R2R?

R2R align sequence reads to a reference sequence using new algorithms. R2R was developed using Illumina sequence data as test data, but will work with any short read sequence data in FASTQ format.

R2R introduces a new class of aligned reads indicative of insertion/deletion (InDel reads).

R2R use the information in Paired End / Mate Pair reads.

R2R utilize the quality information accompanying each nucleotide in a new way to improve precision of mutation/SNP and InDel calls.

R2R is a complete suite that takes you from a reference sequence and sequence data to analysis and visualization of results in your favorite internet-browser.


Description & Manual

Scripts and test-data

The test-data set contains 25000 reads analyzed with phiX174 as a reference sequence.

The analysis shows 5 simple point mutations.

The hsm_3 data set contains ~6 million reads obtained from the E. coli hsm_3 mutant analyzed with E. coli MG1655 as a reference. hsm_3 data set (zip) (642 Mb). Data comes all included: raw data, indexed data, ini-files, html-index files and html panel files so you can re-run analysis (with different setttings) or just enjoy the results. Cheat?


Test if you like R2R:

Click either link below and identify one mutation and one insertion in the sequence data compared to the reference sequence. See the manual if you need further help.

       panel_No  P_Pos   Mut/InDel     #Mut  #Mut+  #Mut- #Match ID_qual Repeat  SNP?  Suggested mutation(s)      Annotation(s)

panel:      547    694   Mutation:       27     15     12      0                        a>g (1.00)          E>E;  ylbE (Pseudogene ...
panel:      547    832   InDel:          24     15      9      0    0.97                                          ylbE (Pseudogene ...
panel:      547    836   InDel:           8      6      2      0    1.02                                          ylbE (Pseudogene ...

Publications using R2R

van Pijkeren JP, Britton RA..
High efficiency recombineering in lactic acid bacteria.
Nucleic Acids Res. (2012) 40:e76.
Skovgaard O, Bak M, Løbner-Olesen A, Tommerup N.
Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing.
Genome Res. (2011) 21:1388-93.
Charbon G, Riber L, Cohen M, Skovgaard O, Fujimitsu K, Katayama T, Løbner-Olesen A.
Suppressors of DnaA(ATP) imposed overinitiation in Escherichia coli.
Mol Microbiol. (2011) 79:914-28.

Contact: olesk@ruc.dk