Paket: racon (1.5.0-3 och andra)

[ Källkod: racon  ]

consensus module for raw de novo DNA assembly of long uncorrected reads

Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.

Racon can be used as a polishing tool after the assembly with either Illumina data or data produced by third generation of sequencing. The type of data inputed is automatically detected.

Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ format and overlaps/alignments between the reads and the contigs in MHAP/PAF/SAM format. Output is a set of polished contigs in FASTA format printed to stdout. All input files can be compressed with gzip.

Racon can also be used as a read error-correction tool. In this scenario, the MHAP/PAF/SAM file needs to contain pairwise overlaps between reads including dual overlaps.

A wrapper script is also available to enable easier usage to the end- user for large datasets. It has the same interface as racon but adds two additional features from the outside. Sequences can be subsampled to decrease the total execution time (accuracy might be lower) while target sequences can be split into smaller chunks and run sequentially to decrease memory consumption. Both features can be run at the same time as well.

Andra paket besläktade med racon

• dep: libc6 (>= 2.34) [ej alpha, arm64, ia64, sh4]

  GNU C-bibliotek: Delade bibliotek
  också ett virtuellt paket som tillhandahålls av libc6-udeb

  dep: libc6 (>= 2.37) [sh4]

  dep: libc6 (>= 2.38) [arm64]

• dep: libc6.1 (>= 2.32) [alpha]

  GNU C-bibliotek: Delade bibliotek
  också ett virtuellt paket som tillhandahålls av libc6.1-udeb

  dep: libc6.1 (>= 2.35) [ia64]

• dep: libedlib1 (>= 1.2.7-3~)

  library for sequence alignment using edit distance

• dep: libgcc-s1 (>= 3.0) [amd64, arm64, i386, mips64el, ppc64, ppc64el, s390x, x32]

  GCC stödbibliotek

  dep: libgcc-s1 (>= 3.4) [alpha, riscv64, sparc64]

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

  dep: libgcc-s1 (>= 4.2) [ia64, sh4]

• dep: libgcc-s2 (>= 4.2.1) [m68k]

  GCC stödbibliotek

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC stödbibliotek

• dep: libspoa7.0.0 (>= 4.0.5) [amd64]

  SIMD partial order alignment library

  dep: libspoa7.0.0 (>= 4.0.7+ds) [alpha, ia64, mips64el, ppc64, ppc64el, s390x, sparc64]

  dep: libspoa7.0.0 (>= 4.0.8) [armel, armhf, hppa, i386, m68k, riscv64, sh4, x32]

  dep: libspoa7.0.0 (>= 4.1.4) [arm64]

• dep: libstdc++6 (>= 12) [alpha, amd64, ia64, mips64el, ppc64, ppc64el, s390x, sparc64]

  GNU standardbibliotek v3 för C++

  dep: libstdc++6 (>= 13.1) [ej alpha, amd64, ia64, mips64el, ppc64, ppc64el, s390x, sparc64]

• dep: libunwind8 [ia64]

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

• dep: zlib1g (>= 1:1.1.4)

  Kompressionsbibliotek - körtidspaket

• rec: python3

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

• rec: rampler

  module for sampling genomic sequences

Hämta racon

Hämtningar för alla tillgängliga arkitekturer

Arkitektur	Version	Paketstorlek	Installerad storlek	Filer
alpha (inofficiell anpassning)	1.5.0-3	3.042,9 kbyte	3.208,0 kbyte	[filförteckning]
amd64	1.5.0-3	3.042,2 kbyte	3.167,0 kbyte	[filförteckning]
arm64	1.5.0-3+b1	3.038,4 kbyte	3.208,0 kbyte	[filförteckning]
armel	1.5.0-3	3.033,8 kbyte	3.150,0 kbyte	[filförteckning]
armhf	1.5.0-3	3.033,6 kbyte	3.110,0 kbyte	[filförteckning]
hppa (inofficiell anpassning)	1.5.0-3	3.042,3 kbyte	3.165,0 kbyte	[filförteckning]
i386	1.5.0-3	3.047,0 kbyte	3.174,0 kbyte	[filförteckning]
ia64 (inofficiell anpassning)	1.5.0-3	3.056,1 kbyte	3.324,0 kbyte	[filförteckning]
m68k (inofficiell anpassning)	1.5.0-3	3.039,8 kbyte	3.158,0 kbyte	[filförteckning]
mips64el	1.5.0-3	3.041,9 kbyte	3.217,0 kbyte	[filförteckning]
ppc64 (inofficiell anpassning)	1.5.0-3	3.046,7 kbyte	3.271,0 kbyte	[filförteckning]
ppc64el	1.5.0-3	3.047,2 kbyte	3.207,0 kbyte	[filförteckning]
riscv64	1.5.0-3+b1	3.040,6 kbyte	3.136,0 kbyte	[filförteckning]
s390x	1.5.0-3	3.038,0 kbyte	3.179,0 kbyte	[filförteckning]
sh4 (inofficiell anpassning)	1.5.0-3	3.049,4 kbyte	3.207,0 kbyte	[filförteckning]
sparc64 (inofficiell anpassning)	1.5.0-3	3.033,1 kbyte	4.042,0 kbyte	[filförteckning]
x32 (inofficiell anpassning)	1.5.0-3	3.042,0 kbyte	3.154,0 kbyte	[filförteckning]