smalt-examples - Sequence Mapping and Alignment Tool (examples)

Distribution: Ubuntu 16.04 LTS (Xenial Xerus)
Repository: Ubuntu Universe i386
Package name: smalt-examples
Package version: 0.7.6
Package release: 4
Package architecture: all
Package type: deb
Installed size: 68.60 KB
Download size: 68.55 MB
Official Mirror:
SMALT efficiently aligns DNA sequencing reads with a reference genome. It 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. This package contains example data and a test suite to test the data.



    Source package: smalt

    Install Howto

    1. Update the package index:
      # sudo apt-get update
    2. Install smalt-examples deb package:
      # sudo apt-get install smalt-examples


    • /usr/share/doc/smalt-examples/changelog.Debian.gz
    • /usr/share/doc/smalt-examples/copyright
    • /usr/share/doc/smalt/test/
    • /usr/share/doc/smalt/test/
    • /usr/share/doc/smalt/test/
    • /usr/share/doc/smalt/test/
    • /usr/share/doc/smalt/test/
    • /usr/share/doc/smalt/test/
    • /usr/share/doc/smalt/test/
    • /usr/share/doc/smalt/test/
    • /usr/share/doc/smalt/test/
    • /usr/share/doc/smalt/test/
    • /usr/share/doc/smalt/test/
    • /usr/share/doc/smalt/test/
    • /usr/share/doc/smalt/test/data/
    • /usr/share/doc/smalt/test/data/Makefile.gz
    • /usr/share/doc/smalt/test/data/
    • /usr/share/doc/smalt/test/data/cigar_read1.fq
    • /usr/share/doc/smalt/test/data/cigar_read2.fq
    • /usr/share/doc/smalt/test/data/cigar_ref.fa.gz
    • /usr/share/doc/smalt/test/data/contigs.fa.gz
    • /usr/share/doc/smalt/test/data/gen1l100i500e1_1.fq
    • /usr/share/doc/smalt/test/data/gen1l100i500e1_2.fq
    • /usr/share/doc/smalt/test/data/gen1l75i300e0_1.fq.gz
    • /usr/share/doc/smalt/test/data/gen1l75i300e0_2.fq.gz
    • /usr/share/doc/smalt/test/data/genome_1.fa.gz
    • /usr/share/doc/smalt/test/data/hs37chrXtrunc.fa.gz
    • /usr/share/doc/smalt/test/data/hs37l100i300e05q_trunc.bam.gz
    • /usr/share/doc/smalt/test/data/hs37l100i300e05q_trunc.sam.gz
    • /usr/share/doc/smalt/test/data/hs37l100i300e05q_trunc_nonam_1.fq.gz
    • /usr/share/doc/smalt/test/data/hs37l100i300e05q_trunc_nonam_2.fq.gz
    • /usr/share/doc/smalt/test/data/sequence_test_1.fa.gz
    • /usr/share/doc/smalt/test/data/sequence_test_2.fa.gz
    • /usr/share/doc/smalt/test/data/sequence_test_3.fq.gz
    • /usr/share/doc/smalt/test/data/sequence_test_4.fq.gz


    See smalt_0.7.6-4_i386.deb changelog.