H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, issue.14, pp.1754-60, 2009.

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nat Methods, vol.9, issue.4, pp.357-366, 2012.

R. Li, C. Yu, Y. Li, T. W. Lam, S. Yiu et al., SOAP2: an improved ultrafast tool for short read alignment, Bioinformatics, vol.25, issue.15, pp.1966-1973, 2009.

P. Ferragina and G. Manzini, Opportunistic data structures with applications, FOCS, pp.390-398, 2000.

M. Burrows and D. J. Wheeler, A block sorting data compression algorithm, 1994.

K. Kimura and A. Koike, Analysis of genomic rearrangements by using the Burrows-Wheeler transform of short-read data, BMC Bioinform, vol.16, p.5, 2015.

K. Kimura and A. Koike, Ultrafast SNP analysis using the Burrows-Wheeler transform of short-read data, Bioinformatics, vol.31, issue.10, pp.1577-83, 2015.

P. Peterlongo, N. Schnel, N. Pisanti, M. Sagot, and V. Lacroix, Identifying SNPs without a reference genome by comparing raw reads, SPIRE, LNCS, vol.6393, pp.147-58, 2010.
URL : https://hal.archives-ouvertes.fr/inria-00514887

G. Sacomoto, J. Kielbassa, R. Chikhi, R. Uricaru, P. Antoniou et al., KISSPLICE: de-novo calling alternative splicing events from RNA-seq data, BMC Bioinform, vol.13, issue.6, p.5, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00784407

R. M. Leggett and D. Maclean, Reference-free SNP detection: dealing with the data deluge, BMC Genom, vol.15, issue.4, p.10, 2014.

Z. Iqbal, I. Turner, G. Mcvean, P. Flicek, and M. Caccamo, De novo assembly and genotyping of variants using colored de Bruijn graphs, Nat Genet, vol.44, issue.2, pp.226-258, 2012.

D. D. Dolle, Z. Liu, M. Cotten, J. T. Simpson, Z. Iqbal et al., Using reference-free compressed data structures to analyze, vol.13, p.13

. Prezza, 14:3 ? fast, convenient online submission ? thorough peer review by experienced researchers in your field ? rapid publication on acceptance ? support for research data, including large and complex data types ? gold Open Access which fosters wider collaboration and increased citations maximum visibility for your research: over 100M website views per year ? At BMC, research is always in progress. Learn more biomedcentral.com/submissions Ready to submit your research ? Choose BMC and benefit from: sequencing reads from thousands of human genomes, Algorithms Mol Biol, vol.27, issue.2, pp.300-309, 2017.

S. Mantaci, A. Restivo, G. Rosone, and M. Sciortino, An extension of the Burrows-Wheeler transform, Theor Comput Sci, vol.387, issue.3, pp.298-312, 2007.

M. J. Bauer, A. J. Cox, and G. Rosone, Lightweight algorithms for constructing and inverting the BWT of string collections, Theor Comput Sci, vol.483, pp.134-182, 2013.

, The 1000 Genomes Project Consortium. A global reference for human genetic variation, Nature, vol.526, pp.68-74, 2015.

A. J. Cox, T. Jakobi, G. Rosone, and O. B. Schulz-trieglaff, Comparing DNA sequence collections by direct comparison of compressed text indexes, WABI, LNBI, vol.7534, pp.214-238, 2012.

C. Ander, O. B. Schulz-trieglaff, J. Stoye, and A. J. Cox, metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences, BMC Bioinform, vol.14, issue.5, p.2, 2013.

N. Philippe, M. Salson, T. Lecroq, M. Léonard, T. Commes et al., Querying large read collections in main memory: a versatile data structure, BMC Bioinform, vol.12, p.242, 2011.
URL : https://hal.archives-ouvertes.fr/lirmm-00632958

N. Välimäki and E. Rivals, Scalable and versatile k-mer Indexing for highthroughput sequencing data, ISBRA, LNCS, vol.7875, pp.237-285, 2013.

T. M. Kowalski, S. Grabowski, and S. Deorowicz, Indexing arbitrary-length k-mers in sequencing reads, PLoS ONE, vol.10, issue.7, p.133198, 2015.

J. Schröder, H. Schröder, S. J. Puglisi, R. Sinha, and B. Schmidt, SHREC: a short-read error correction method, Bioinformatics, vol.25, issue.17, pp.2157-63, 2009.

C. Lemaitre, L. Ciortuz, and P. Peterlongo, Mapping-free and assembly-free discovery of inversion breakpoints from raw NGS reads, pp.119-149, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01063157

E. Birmelé, P. Crescenzi, R. A. Ferreira, R. Grossi, V. Lacroix et al., Efficient bubble enumeration in directed graphs, SPIRE, LNCS, vol.7608, pp.118-147, 2012.

R. M. Leggett, R. H. Ramirez-gonzalez, W. Verweij, C. G. Kawashima, Z. Iqbal et al., Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de Bruijn graphs, PLoS ONE, vol.8, issue.3, pp.1-11, 2013.

R. Uricaru, G. Rizk, V. Lacroix, E. Quillery, O. Plantard et al., Reference-free detection of isolated SNPs, Nucl Acids Res, vol.43, issue.2, p.11, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01083715

P. Peterlongo, C. Riou, E. Drezen, and C. Lemaitre, DiscoSnp++: de novo detection of small variants from raw unassembled read set(s). bioRxiv, 2017.

S. N. Gardner and B. G. Hall, When whole-genome alignments just won't work: kSNP v2 Software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes, PLoS ONE, vol.8, issue.12, p.81760, 2013.

N. Prezza, N. Pisanti, M. Sciortino, and G. Rosone, Detecting mutations by eBWT, WABI 2018, Leibniz international proceedings in informatics (LIPIcs), vol.113, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01925950

F. Shi, Suffix arrays for multiple strings: a method for on-line multiple string searches, ASIAN, LNCS, vol.1179, pp.11-22, 1996.

A. J. Cox, F. Garofalo, G. Rosone, and M. Sciortino, Lightweight LCP construction for very large collections of strings, J Discrete Algorithms, vol.37, pp.17-33, 2016.

F. A. Louza, G. P. Telles, S. Hoffmann, and C. Ciferri, Generalized enhanced suffix array construction in external memory, Algorithms Mol Biol, vol.12, issue.1, p.26, 2017.

U. Manber and G. Myers, Suffix arrays: a new method for on-line string searches, SODA, pp.319-346, 1990.

L. Egidi and G. Manzini, Lightweight BWT and LCP merging via the Gap algorithm, SPIRE, LNCS, vol.10508, pp.176-90, 2017.

M. Schirmer, D. '-amore, R. Ijaz, U. Z. Hall, N. Quince et al., Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data, BMC Bioinform, vol.17, issue.1, p.125, 2016.

F. A. Louza, S. Gog, and G. P. Telles, Inducing enhanced suffix arrays for string collections, Theor Comput Sci, vol.678, pp.22-39, 2017.

H. Li and R. Durbin, Fast and accurate long-read alignment with Burrows-Wheeler transform, Bioinformatics, vol.26, issue.5, pp.589-95, 2010.

D. A. Earl, K. Bradnam, J. S. John, A. Darling, D. Lin et al., Assemblathon 1: a competitive assessment of de novo short read assembly methods, Gen Res, vol.21, issue.12, pp.2224-2265, 2011.
URL : https://hal.archives-ouvertes.fr/inria-00637571