Paket: segemehl (0.3.4-3)

[ Källkod: 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.

Märken: Interface Toolkit: Ncurses TUI

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Hämta segemehl

Hämtningar för alla tillgängliga arkitekturer

Arkitektur	Paketstorlek	Installerad storlek	Filer
amd64	285,6 kbyte	1.215,0 kbyte	[filförteckning]
arm64	258,9 kbyte	1.151,0 kbyte	[filförteckning]
armel	235,4 kbyte	1.089,0 kbyte	[filförteckning]
armhf	233,0 kbyte	737,0 kbyte	[filförteckning]
i386	310,0 kbyte	1.425,0 kbyte	[filförteckning]
mips64el	263,1 kbyte	1.420,0 kbyte	[filförteckning]
mipsel	278,5 kbyte	1.409,0 kbyte	[filförteckning]
ppc64el	310,6 kbyte	1.623,0 kbyte	[filförteckning]
s390x	260,5 kbyte	1.322,0 kbyte	[filförteckning]