30 citations · 34 across the 3 of their papers we have counts for
4 papers · 1 filter
Parallel decompression of gzip-compressed files and random access to DNA sequences
Maël Kerbiriou, Rayan Chikhi
Decompressing a file made by the gzip program at an arbitrary location is in principle impossible, due to the nature of the DEFLATE compression algorithm. Consequently, no existing…
Data structures to represent a set of k-long DNA sequences
Rayan Chikhi, Jan Holub, Paul Medvedev
The analysis of biological sequencing data has been one of the biggest applications of string algorithms. The approaches used in many such applications are based on the analysis of…
Dualities in Tree Representations
Rayan Chikhi, Alexander Schönhuth
A characterization of the tree such that , the reversal of is given. An immediate consequence is…
Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-Linear Chaining Extended
Anna Kuosmanen, Topi Paavilainen, Travis Gagie +3
Aligning sequencing reads on graph representations of genomes is an important ingredient of pan-genomics. Such approaches typically find a set of local anchors that indicate plausi…