パッケージ: wtdbg2 (2.5-10)
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.
その他の wtdbg2 関連パッケージ
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- dep: libc6 (>= 2.34)
- GNU C ライブラリ: 共有ライブラリ
以下のパッケージによって提供される仮想パッケージでもあります: libc6-udeb
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- dep: zlib1g (>= 1:1.2.0)
- 圧縮ライブラリ - ランタイム
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- sug: minimap2
- versatile pairwise aligner for genomic and spliced nucleotide sequences
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- sug: mummer
- 遺伝子全体の効率的な配列アライメント
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- sug: perl
- Larry Wall 作の実用的な抽出とレポート用の言語
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- sug: samtools
- processing sequence alignments in SAM, BAM and CRAM formats
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- sug: wtdbg2-examples
- Examples for wtdbg - de novo sequence assembler