Package: wtdbg2 (2.5-9 and others)

[ Source: wtdbg2  ]

de novo sequence assembler for long noisy reads

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 correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.

During assembly, wtdbg2 chops reads into 1024bp segments, merges similar segments into a vertex and connects vertices based on the segment adjacency on reads. The resulting graph is called fuzzy Bruijn graph (FBG). It is akin to De Bruijn graph but permits mismatches/gaps and keeps read paths when collapsing k-mers. The use of FBG distinguishes wtdbg2 from the majority of long-read assemblers.

Other Packages Related to wtdbg2

• dep: libc6 (>= 2.34) [amd64]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

• dep: libc6.1 (>= 2.31) [ia64]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6.1-udeb

• dep: libunwind8 [ia64]

  library to determine the call-chain of a program - runtime

• dep: zlib1g (>= 1:1.2.0)

  compression library - runtime

• sug: minimap2

  versatile pairwise aligner for genomic and spliced nucleotide sequences

• sug: mummer

  Efficient sequence alignment of full genomes

• sug: perl

  Larry Wall's Practical Extraction and Report Language

• sug: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

• sug: wtdbg2-examples

  Examples for wtdbg - de novo sequence assembler

Download wtdbg2

Download for all available architectures

Architecture	Version	Package Size	Installed Size	Files
amd64	2.5-9	680.7 kB	6,810.0 kB	[list of files]
ia64 (unofficial port)	2.5-8	500.8 kB	2,364.0 kB	[list of files]