Jabba: Hybrid Error Correction for Long Sequencing Reads
...ion (PacBio / ONT) sequencing data, using second generation (Illumina) data. Input Jabba takes as input a concatenated de Bruijn graph and a set of sequences: the de Bruijn graph should appear in fasta...1995 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps betw...2206 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
...s the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called red-black multipositional de Bruijn graph to detect misassemblies...2143 days ago
FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform
...ncing data, FMLRC will build an FM-index and use that as an implicit de Bruijn graph. Each long read is then...them with the closest matching high frequency k-mers in the implicit de Bruijn graph. In contrast to other d...2108 days ago
LoRMA: A tool for correcting sequencing errors in long reads
...ction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length...2081 days ago
2012 days ago
wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error cor...1930 days ago
Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
...ously. **experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compiler only Cycles enumeration (aka Bubbles) as part of de novo de bruijn graphs assembly using colours...1572 days ago
GRIDSS: the Genomic Rearrangement IDentification Software Suite
...nd assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end a...1462 days ago
JumboDB: tool for de Bruijn graph construction
jumboDB tool for fast de Bruijn graph construction from long sequences (reads or genomes) with very low...ut rather a subroutine that translates a set of reads into compressed de Bruijn graph. More at https://...1005 days ago