Package: minia (3.2.6-3)

[ Source: 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).

Other Packages Related to minia

• dep: bc

  GNU bc arbitrary precision calculator language

• dep: libc6 (>= 2.34)

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

• dep: libgatbcore3 (>= 1.4.2) [amd64]

  dynamic library of the Genome Analysis Toolbox

  dep: libgatbcore3 (>= 1.4.2+dfsg) [not amd64]

• dep: libgcc-s1 (>= 3.0)

  GCC support library

• dep: libhdf5-103-1

  HDF5 C runtime files - serial version

• dep: libstdc++6 (>= 11)

  GNU Standard C++ Library v3

• dep: zlib1g

  compression library - runtime

• rec: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

• sug: bandage

  Bioinformatics Application for Navigating De novo Assembly Graphs Easily

Download minia

Download for all available architectures

Architecture	Package Size	Installed Size	Files
amd64	393.2 kB	740.0 kB	[list of files]
arm64	385.1 kB	824.0 kB	[list of files]
mips64el	383.2 kB	843.0 kB	[list of files]
ppc64el	393.8 kB	824.0 kB	[list of files]