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Package: staden (2.0.0+b11-4build1)

DNA sequence assembly (Gap4/Gap5), editing and analysis tools

Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin).

Gap4 performs sequence assembly, contig ordering based on read pair data, contig joining based on sequence comparisons, assembly checking, repeat searching, experiment suggestion, read pair analysis and contig editing. It has graphical views of contigs, templates, readings and traces which all scroll in register. Contig editor searches and experiment suggestion routines use confidence values to calculate the confidence of the consensus sequence and hence identify only places requiring visual trace inspection or extra data. The result is extremely rapid finishing and a consensus of known accuracy.

Pregap4 provides a graphical user interface to set up the processing required to prepare trace data for assembly or analysis, and automates these processes.

Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and ZTR trace files.

Prefinish analyses partially completed sequence assemblies and suggests the most efficient set of experiments to help finish the project.

Tracediff and hetscan automatically locate mutations by comparing trace data against reference traces. They annotate the mutations found ready for viewing in gap4.

Spin analyses nucleotide sequences to find genes, restriction sites, motifs, etc. It can perform translations, find open reading frames, count codons, etc. Many results are presented graphically and a sliding sequence window is linked to the graphics cursor. Spin also compares pairs of sequences in many ways. It has very rapid dot matrix analysis, global and local alignment algorithms, plus a sliding sequence window linked to the graphical plots. It can compare nucleic acid against nucleic acid, protein against protein, and protein against nucleic acid.

Other Packages Related to staden

  • depends
  • recommends
  • suggests
  • dep: libc6 (>= 2.29)
    GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb
  • dep: libgcc-s1 (>= 3.0) [amd64]
    GCC support library
    dep: libgcc-s1 (>= 3.5) [armhf]
  • dep: liblzma5 (>= 5.1.1alpha+20120614)
    XZ-format compression library
  • dep: libpng16-16 (>= 1.6.2-1)
    PNG library - runtime (version 1.6)
  • dep: libstaden-read13
    Staden library for reading and writing DNA sequencing results
  • dep: libstdc++6 (>= 5)
    GNU Standard C++ Library v3
  • dep: libtcl8.6 (>= 8.6.0)
    Tcl (the Tool Command Language) v8.6 - run-time library files
  • dep: libtk8.6 (>= 8.6.0)
    Tk toolkit for Tcl and X11 v8.6 - run-time files
  • dep: libx11-6
    X11 client-side library
  • dep: staden-common (= 2.0.0+b11-4build1)
    Architecture independent files for Staden
  • dep: staden-io-lib-utils
    programs for manipulating DNA sequencing files
  • dep: tklib
    standard Tk Library
  • dep: zlib1g (>= 1:1.1.4)
    compression library - runtime
  • rec: med-config (>= 2.1)
    Debian Med general config package

Download staden

Download for all available architectures
Architecture Package Size Installed Size Files
amd64 1,379.3 kB4423 kB [list of files]
armhf 1,187.5 kB2788 kB [list of files]