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パッケージ: smalt (0.7.6-7)

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smalt

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Sequence Mapping and Alignment Tool

SMALT efficiently aligns DNA sequencing reads with a reference genome. Reads from a wide range of sequencing platforms, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including paired reads.

The software employs a perfect hash index of short words (< 20 nucleotides long), sampled at equidistant steps along the genomic reference sequences.

For each read, potentially matching segments in the reference are identified from seed matches in the index and subsequently aligned with the read using a banded Smith-Waterman algorithm.

The best gapped alignments of each read is reported including a score for the reliability of the best mapping. The user can adjust the trade-off between sensitivity and speed by tuning the length and spacing of the hashed words.

A mode for the detection of split (chimeric) reads is provided. Multi-threaded program execution is supported.

その他の smalt 関連パッケージ

  • 依存
  • 推奨
  • 提案
  • dep: libbambamc0
    Runtime library for reading and writing BAM (genome alignment) files
  • dep: libc6 (>= 2.14) [amd64]
    GNU C Library: Shared libraries
    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
    dep: libc6 (>= 2.7) [i386]
  • dep: zlib1g (>= 1:1.2.0.2)
    compression library - runtime

smalt のダウンロード

すべての利用可能アーキテクチャ向けのダウンロード
アーキテクチャ パッケージサイズ インストールサイズ ファイル
amd64 110.5 kB289 kB [ファイル一覧]
i386 123.4 kB328 kB [ファイル一覧]