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Protocols

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SMALT specifications

Information


Unique identifier OMICS_00686
Name SMALT
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 in pipelines

 (44)
2018
PMCID: 5956992
PMID: 29678234
DOI: 10.1016/j.vetimm.2018.03.004

[…] for the genomes of 16 t. parva isolates for which data is available in the european nucleotide archive (ena) were mapped to the re-annotated t. parva muguga reference genome (cited in ) using the smalt short read aligner (www.sanger.ac.uk/resources/software/smalt) set at default settings. duplicates were marked using picard tools (http://broadinstitute.github.io/picard) set at default […]

2017
PMCID: 5282449
PMID: 28197136
DOI: 10.3389/fmicb.2017.00073

[…] into contigs using spades (bankevich et al., )., 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 (https://sourceforge.net/projects/smalt/). smalt was chosen because we have already observed that it performed well with low coverages and when using distant references (pightling et […]

2017
PMCID: 5335918
PMID: 28131954
DOI: 10.1016/j.micpath.2017.01.042

[…] illumina hiseq® or miseq® sequencing technology, respectively. de novo draft assemblies were created using velvet v1.2.08 or v1.2.10 and sequencing reads were mapped to the reference genome using smalt v.0.6.4 and v.0.7.4 . snps and indels were called using samtools mpileup ., standard methods were used for molecular cloning . chromosomal and plasmid dna purification, dna modification […]

2017
PMCID: 5349684
PMID: 28253375
DOI: 10.1371/journal.ppat.1006252

[…] 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 (http://www.sanger.ac.uk/science/tools/smalt-0). one region of ambiguous assembly was amplified by pcr and sequenced using sanger methodology to confirm the assembly. a nucleotide deletion […]

2017
PMCID: 5358916
PMID: 28223459
DOI: 10.1128/mBio.01976-16

[…] we took the output from prokka and analyzed it with roary ()., we mapped the short reads against the reference genome of k. pneumoniae ecl8 (genbank accession no. hf536482 and canh01000000) with smalt v 0.7.4 (https://www.sanger.ac.uk/resources/software/smalt/). we employed a conservative minimum score of 30 for mapping and then annotated snps with a combination of samtools mpileup () […]


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SMALT in publications

 (253)
PMCID: 5943296
PMID: 29743642
DOI: 10.1038/s41598-018-25764-3

[…] data)., 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, http://www.sanger.ac.uk/science/tools/smalt-0) to reference genomes (s. flexneri 2a 2457 t, s. sonnei 53 g), followed by removal of mobile (plasmids, insertion sequences, other described […]

PMCID: 5956992
PMID: 29678234
DOI: 10.1016/j.vetimm.2018.03.004

[…] for the genomes of 16 t. parva isolates for which data is available in the european nucleotide archive (ena) were mapped to the re-annotated t. parva muguga reference genome (cited in ) using the smalt short read aligner (www.sanger.ac.uk/resources/software/smalt) set at default settings. duplicates were marked using picard tools (http://broadinstitute.github.io/picard) set at default […]

PMCID: 5936940
PMID: 29765675
DOI: 10.1098/rsos.172212

[…] the gap where the gap length was known (less than 100 bp). if the gap length was unknown (greater than 100 bp), the gene was extended to the nearest start or stop codon., by mapping the reads with smalt v5.7 (www.sanger.ac.uk/resources/software/smalt/) to l. braziliensis m2904, the coverage at each site was determined to quantify the chromosome copy numbers and rdaf distributions […]

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 (https://sourceforge.net/projects/smalt/). in order to reduce cpu time, we shredded each tumor assembly into 1 kilobase fragments while removing ‘n’ bases, prior to alignment […]

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

[…] 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 […]


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