Paket: minia (3.2.6-4 und andere)

[ Quellcode: minia  ]

short-read biological sequence assembler

What was referred to as "next-generation" DNA sequencing up to the year 2020 delivered only "short" reads up to ~600 base pairs in length that would then have to be puzzled by random overlaps in their sequence towards a complete genome. This is the genome assembly. And there are many biological pitfalls on long stretches of low complexity regions and copy number variations and other sorts of redundancies that render this difficult.

This package provides a short-read DNA sequence assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.

The output of Minia is a set of contigs, i.e. stretches of gap-free linear overlaps of short reads. In the best possible case this is a whole chromosome.

Minia produces results of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet).

Andere Pakete mit Bezug zu minia

• dep: bc

  GNU bc - Rechnersprache mit beliebiger Genauigkeit

• dep: libc6 (>= 2.34)

  GNU-C-Bibliothek: Laufzeitbibliotheken
  auch ein virtuelles Paket, bereitgestellt durch libc6-udeb

• dep: libgatbcore3 (>= 1.4.2+dfsg)

  dynamic library of the Genome Analysis Toolbox

• dep: libgcc-s1 (>= 3.0)

  GCC Support-Bibliothek

• dep: libhdf5-103-1t64

  Hierarchisches Datenformat 5 (HDF5) - C-Laufzeitdateien - serielle Version

• dep: libstdc++6 (>= 13.1)

  GNU-Implementierung der Standard-C++-Bibliothek (Version 3)

• dep: zlib1g

  Kompressions-Bibliothek - Laufzeit

• rec: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

• sug: bandage

  Bioinformatics Application for Navigating De novo Assembly Graphs Easily

minia herunterladen

Download für alle verfügbaren Architekturen

Architektur	Version	Paketgröße	Größe (installiert)	Dateien
ppc64el	3.2.6-4+b1	392,5 kB	825,0 kB	[Liste der Dateien]