SMALT pipeline

SMALT specifications


Unique identifier OMICS_00686
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA, FASTQ
Output data The output is written to the file map.sam in SAM output format using soft clipping of sequences.
Output format SAM
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 0.7.6
Stability Stable
Maintained Yes



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  • person_outline Hannes Ponstingl <>

SMALT citations

PMCID: 5554395

[…] national center for biotechnology information (ncbi). to detect miss-assemblies, raw data were mapped back against the genome assemblies using smalt v.0.5.8 (; last accessed july 24, 2017). all sequencing data have been deposited at the european nucleotide archive (ena) (; last accessed july 24, 2017) under the accession […]

PMCID: 5467800

[…] for each sample using the contigs, filling gaps with a set of standard whole-genome hiv sequences [51] for positions not covered by the contigs. reads were mapped to these custom references using smalt [52]. the consensus base at each position was called, resulting in a single consensus hiv sequence for each sample. a consensus base was called at each position where coverage exceeded 30 reads […]

PMCID: 5349684

[…] most complete coverage of the reference genome was selected for finishing and downstream analysis. the quality of each scaffold was verified by remapping the untrimmed reads to the assembly using smalt ( one region of ambiguous assembly was amplified by pcr and sequenced using sanger methodology to confirm the assembly. a nucleotide deletion […]

PMCID: 5282449

[…] contigs using spades (bankevich et al., 2012)., additionally, the previously identified closed genome with the highest number of associated reads was then used in a reference guided assembly using smalt v 0.7.4 ( smalt was chosen because we have already observed that it performed well with low coverages and when using distant references (pightling et […]

PMCID: 5047355

[…] (wtsi). for each isolate sequenced, the raw sequence read pairs were split to reduce the overall memory usage and allow reads to be aligned using more than one cpu. the reads were then aligned using smalt, a hashing based sequence aligner. the aligned and unmapped reads were combined into a single bam file. picard was used to identify and flag optical duplicates generated during the making […]

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