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LoRDEC: accurate and efficient long read error correction.
Salmela L, Rivals E. Salmela L, et al. Bioinformatics. 2014 Dec 15;30(24):3506-14. doi: 10.1093/bioinformatics/btu538. Epub 2014 Aug 26. Bioinformatics. 2014. PMID: 25165095 Free PMC article.
Correction of sequencing errors in a mixed set of reads.
Salmela L. Salmela L. Bioinformatics. 2010 May 15;26(10):1284-90. doi: 10.1093/bioinformatics/btq151. Epub 2010 Apr 8. Bioinformatics. 2010. PMID: 20378555
AVAILABILITY: The JAVA source code is freely available at http://www.cs.helsinki.fi/u/lmsalmel/hybrid-shrec/ CONTACT: leena.salmela@cs.helsinki.fi...
AVAILABILITY: The JAVA source code is freely available at http://www.cs.helsinki.fi/u/lmsalmel/hybrid-shrec/ CONTACT: leena.salmela@c …
Correcting errors in short reads by multiple alignments.
Salmela L, Schröder J. Salmela L, et al. Bioinformatics. 2011 Jun 1;27(11):1455-61. doi: 10.1093/bioinformatics/btr170. Epub 2011 Apr 5. Bioinformatics. 2011. PMID: 21471014
Fast scaffolding with small independent mixed integer programs.
Salmela L, Mäkinen V, Välimäki N, Ylinen J, Ukkonen E. Salmela L, et al. Bioinformatics. 2011 Dec 1;27(23):3259-65. doi: 10.1093/bioinformatics/btr562. Epub 2011 Oct 13. Bioinformatics. 2011. PMID: 21998153 Free PMC article.
CONTACT: leena.salmela@cs.helsinki.fi....
CONTACT: leena.salmela@cs.helsinki.fi....
Normalized N50 assembly metric using gap-restricted co-linear chaining.
Mäkinen V, Salmela L, Ylinen J. Mäkinen V, et al. Among authors: salmela l. BMC Bioinformatics. 2012 Oct 3;13:255. doi: 10.1186/1471-2105-13-255. BMC Bioinformatics. 2012. PMID: 23031320 Free PMC article.
Colib'read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads.
Le Bras Y, Collin O, Monjeaud C, Lacroix V, Rivals É, Lemaitre C, Miele V, Sacomoto G, Marchet C, Cazaux B, Zine El Aabidine A, Salmela L, Alves-Carvalho S, Andrieux A, Uricaru R, Peterlongo P. Le Bras Y, et al. Among authors: salmela l. Gigascience. 2016 Feb 11;5:9. doi: 10.1186/s13742-015-0105-2. eCollection 2016. Gigascience. 2016. PMID: 26870323 Free PMC article.
Gap Filling as Exact Path Length Problem.
Salmela L, Sahlin K, Mäkinen V, Tomescu AI. Salmela L, et al. J Comput Biol. 2016 May;23(5):347-61. doi: 10.1089/cmb.2015.0197. Epub 2016 Mar 9. J Comput Biol. 2016. PMID: 26959081
Accurate self-correction of errors in long reads using de Bruijn graphs.
Salmela L, Walve R, Rivals E, Ukkonen E. Salmela L, et al. Bioinformatics. 2017 Mar 15;33(6):799-806. doi: 10.1093/bioinformatics/btw321. Bioinformatics. 2017. PMID: 27273673 Free PMC article.
CONTACT: leena.salmela@cs.helsinki.fi....
CONTACT: leena.salmela@cs.helsinki.fi....
Variant genotyping with gap filling.
Walve R, Salmela L, Mäkinen V. Walve R, et al. Among authors: salmela l. PLoS One. 2017 Sep 8;12(9):e0184608. doi: 10.1371/journal.pone.0184608. eCollection 2017. PLoS One. 2017. PMID: 28886164 Free PMC article.
Error correcting optical mapping data.
Mukherjee K, Washimkar D, Muggli MD, Salmela L, Boucher C. Mukherjee K, et al. Among authors: salmela l. Gigascience. 2018 Jun 1;7(6):giy061. doi: 10.1093/gigascience/giy061. Gigascience. 2018. PMID: 29846578 Free PMC article.
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