Package: centrifuge (1.0.3-12 and others)

[ Source: centrifuge  ]

rapid and memory-efficient system for classification of DNA sequences

Centrifuge is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (e.g., 4.3 GB for ~4,100 bacterial genomes) yet provides very fast classification speed, allowing it to process a typical DNA sequencing run within an hour. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers.

Other Packages Related to centrifuge

• dep: hisat2

  graph-based alignment of short nucleotide reads to many genomes

• dep: jellyfish

  count k-mers in DNA sequences

• dep: libc6 (>= 2.34) [not ia64]

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

• dep: libc6.1 (>= 2.37) [ia64]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6.1-udeb

• dep: libgcc-s1 (>= 3.0) [not hppa, ia64, riscv64]

  GCC support library

  dep: libgcc-s1 (>= 3.4) [riscv64]

  dep: libgcc-s1 (>= 4.2) [ia64]

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC support library

• dep: libstdc++6 (>= 11) [hppa]

  GNU Standard C++ Library v3

  dep: libstdc++6 (>= 13.1) [not hppa]

• dep: libunwind8 [ia64]

  library to determine the call-chain of a program - runtime

• dep: python3

  interactive high-level object-oriented language (default python3 version)

Download centrifuge

Download for all available architectures

Architecture	Version	Package Size	Installed Size	Files
amd64	1.0.3-12	551.6 kB	1,711.0 kB	[list of files]
arm64	1.0.3-12	506.3 kB	1,597.0 kB	[list of files]
hppa (unofficial port)	1.0.3-11	597.6 kB	1,679.0 kB	[list of files]
ia64 (unofficial port)	1.0.3-12	779.7 kB	3,011.0 kB	[list of files]
mips64el	1.0.3-12	529.9 kB	1,893.0 kB	[list of files]
ppc64el	1.0.3-12	564.4 kB	1,789.0 kB	[list of files]
riscv64	1.0.3-12	586.5 kB	1,405.0 kB	[list of files]