软件包：segemehl（0.3.4-5 以及其他的）

[ 源代码： segemehl  ]

short read mapping with gaps

Segemehl is a software to map short sequencer reads to reference genomes. Segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl accepts fasta and fastq queries (gzip'ed and bgzip'ed). In addition to the alignment of reads from standard DNA- and RNA-seq protocols, it also allows the mapping of bisulfite converted reads (Lister and Cokus) and implements a split read mapping strategy. The output of segemehl is a SAM or BAM formatted alignment file. In the case of split-read mapping, additional BED files are written to the disc. These BED files may be summarized with the postprocessing tool haarz. In the case of the alignment of bisulfite converted reads, raw methylation rates may also be called with haarz.

In brief, for each suffix of a read, segemehl aims to find the best-scoring seed. Seeds might contain insertions, deletions, and mismatches (differences). The number of differences allowed within a single seed is user-controlled and is crucial for the runtime of the program. Subsequently, seeds that undercut the user-defined E-value are passed on to an exact semi-global alignment procedure. Finally, reads with a minimum accuracy of percent are reported to the user.

标签: 界面工具箱: Ncurses TUI

其他与 segemehl 有关的软件包

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

  GNU C 语言运行库：共享库
  同时作为一个虚包由这些包填实： libc6-udeb

  dep: libc6 (>= 2.37) [sh4]

• dep: libc6.1 (>= 2.34) [alpha]

  GNU C 语言运行库：共享库
  同时作为一个虚包由这些包填实： libc6.1-udeb

  dep: libc6.1 (>= 2.37) [ia64]

• dep: libhts3t64 (>= 1.17)

  C library for high-throughput sequencing data formats

• dep: libncurses6 (>= 6) [sparc64]

  终端控制的共享库

• dep: libtinfo6 (>= 6) [sparc64]

  用于终端处理的共享底层 terminfo 库

• dep: zlib1g (>= 1:1.2.2.4)

  压缩库 - 运行时

下载 segemehl

下载可用于所有硬件架构的

硬件架构	版本	软件包大小	安装后大小	文件
alpha （非官方移植版）	0.3.4-5+b1	294.4 kB	1,569.0 kB	[文件列表]
amd64	0.3.4-5+b1	302.7 kB	1,283.0 kB	[文件列表]
arm64	0.3.4-5+b2	271.4 kB	1,311.0 kB	[文件列表]
armel	0.3.4-5+b1	246.1 kB	1,137.0 kB	[文件列表]
armhf	0.3.4-5+b1	242.0 kB	777.0 kB	[文件列表]
hppa （非官方移植版）	0.3.4-5+b1	280.4 kB	1,221.0 kB	[文件列表]
i386	0.3.4-5+b1	318.5 kB	1,461.0 kB	[文件列表]
ia64 （非官方移植版）	0.3.4-5+b1	360.4 kB	2,550.0 kB	[文件列表]
m68k （非官方移植版）	0.3.4-5+b1	250.2 kB	1,125.0 kB	[文件列表]
mips64el	0.3.4-5+b1	274.3 kB	1,520.0 kB	[文件列表]
ppc64 （非官方移植版）	0.3.4-5+b1	313.5 kB	1,823.0 kB	[文件列表]
ppc64el	0.3.4-5+b1	321.4 kB	1,695.0 kB	[文件列表]
riscv64	0.3.4-5+b2	305.2 kB	1,011.0 kB	[文件列表]
s390x	0.3.4-5+b1	317.9 kB	1,530.0 kB	[文件列表]
sh4 （非官方移植版）	0.3.4-5+b1	314.5 kB	1,053.0 kB	[文件列表]
sparc64 （非官方移植版）	0.3.4-5+b1	232.1 kB	2,087.0 kB	[文件列表]
x32 （非官方移植版）	0.3.4-5+b1	308.2 kB	1,285.0 kB	[文件列表]