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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




No version available


  • person_outline Hannes Ponstingl

SMALT citations


Genomic epidemiology of Shigella in the UK shows transmission of pathogen sublineages and determinants of antimicrobial resistance

Sci Rep
PMCID: 5943296
PMID: 29743642
DOI: 10.1038/s41598-018-25764-3

[…] DNA was extracted and isolates whole genome sequenced as previously described. Whole genome sequence phylogenetic trees were constructed through mapping of sequence data (using smalt, to reference genomes (S. flexneri 2a 2457 T, S. sonnei 53 G), followed by removal of mobile (plasmids, insertion sequences, other described mobile […]


Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus

R Soc Open Sci
PMCID: 5936940
PMID: 29765675
DOI: 10.1098/rsos.172212

[…] The filtered reads with Smalt as mapped above were used for calling SNPs using Samtools Pileup v0.1.11 and Mpileup v0.1.18 and quality-filtered with Vcftools v0.1.12b and Bcftools v0.1.17-dev as previously [] such that SNPs […]


The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils

Cancer Cell
PMCID: 5896245
PMID: 29634948
DOI: 10.1016/j.ccell.2018.03.013

[…] were present one or more of the four tumor de novo assemblies, but which were absent from the reference genome. We first built an alignment index for absence in the reference assembly Devil7.1 using SMALT ( In order to reduce CPU time, we shredded each tumor assembly into 1 kilobase fragments while removing ‘N’ bases, prior to alignment against the indexed […]


The impact of serotype specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan genome

PLoS Pathog
PMCID: 5902063
PMID: 29617440
DOI: 10.1371/journal.ppat.1006966

[…] e Ns [,]. Final contigs were ordered using Mauve, manually curated using ACT, and concatenated []. Filtered Illumina reads from isolates comprising each SC were mapped to the selected reference using SMALT v0.7.6 and SNPs were identified using SAMtools v1.3.1 []. SNPs were filtered requiring a depth of coverage of five and a minimum alternate allele frequency of 0.75. The output was analyzed as pr […]


Phylogenetic analyses and antimicrobial resistance profiles of Campylobacter spp. from diarrhoeal patients and chickens in Botswana

PLoS One
PMCID: 5862492
PMID: 29561903
DOI: 10.1371/journal.pone.0194481

[…] bootstrapping mode [], and visualised in the interactive Tree of life tool (iTol) []. For SNP-based phylogenies, sequence reads were aligned against C. jejuni NCTC11168 [] as a reference genome using SMALT [], following default settings to identify SNPs. Extracted SNPs were used to construct ML-phylogenies using RaxML v 7.3.6 (rapid bootstrapping and subsequent ML search using 100 bootstrap replic […]


Pseudomonas aeruginosa intensive care unit outbreak: winnowing of transmissions with molecular and genomic typing

PMCID: 5840502
PMID: 29229490
DOI: 10.1016/j.jhin.2017.12.005
call_split See protocol

[…] (Illumina Inc, San Diego, CA, USA) using a resequencing workflow. The Illumina sequences generated were deposited in the European Nucleotide Archive under the study accession number ERP023446. Using SMALT (Wellcome Trust Sanger Institute;, reads were initially mapped to the chromosome of P. aeruginosa PAO1 (accession number AE004091), and single nucleot […]


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