Pakket: smalt (0.7.6-9)

[ Bron: smalt  ]

Sequence Mapping and Alignment Tool

SMALT efficiently aligns DNA sequencing reads with a reference genome. Reads from a wide range of sequencing platforms, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including paired reads.

The software employs a perfect hash index of short words (< 20 nucleotides long), sampled at equidistant steps along the genomic reference sequences.

For each read, potentially matching segments in the reference are identified from seed matches in the index and subsequently aligned with the read using a banded Smith-Waterman algorithm.

The best gapped alignments of each read is reported including a score for the reliability of the best mapping. The user can adjust the trade-off between sensitivity and speed by tuning the length and spacing of the hashed words.

A mode for the detection of split (chimeric) reads is provided. Multi-threaded program execution is supported.

Andere aan smalt gerelateerde pakketten

• dep: libbambamc0

  Runtime library for reading and writing BAM (genome alignment) files

• dep: libc6 (>= 2.29)

  GNU C Bibliotheek: Gedeelde bibliotheken
  Ook een virtueel pakket geboden door: libc6-udeb

• dep: zlib1g (>= 1:1.2.0.2)

  compressiebibliotheek - programma's

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Pakket downloaden voor alle beschikbare platforms

Platform	Pakketgrootte	Geïnstalleerde grootte	Bestanden
amd64	110,5 kB	299,0 kB	[overzicht]
arm64	101,2 kB	283,0 kB	[overzicht]
armel	96,2 kB	265,0 kB	[overzicht]
armhf	95,7 kB	197,0 kB	[overzicht]
i386	122,1 kB	333,0 kB	[overzicht]
mips64el	106,7 kB	340,0 kB	[overzicht]
mipsel	112,5 kB	337,0 kB	[overzicht]
ppc64el	120,1 kB	407,0 kB	[overzicht]
s390x	103,3 kB	315,0 kB	[overzicht]