SMALT protocols

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SMALT computational protocol

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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Maintainer


  • person_outline Hannes Ponstingl <>

SMALT IN pipelines

 (38)
2017
PMCID: 5282449
PMID: 28197136
DOI: 10.3389/fmicb.2017.00073

[…] 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 (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

[…] hiseq® or miseq® sequencing technology, respectively. de novo draft assemblies were created using velvet v1.2.08 or v1.2.10 [21] and sequencing reads were mapped to the reference genome using smalt v.0.6.4 and v.0.7.4 [22]. snps and indels were called using samtools mpileup [23]., standard methods were used for molecular cloning [24]. chromosomal and plasmid dna purification, dna […]

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

[…] 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 within a homopolymer run in the m153r gene […]

2017
PMCID: 5467800
PMID: 28604782
DOI: 10.1371/journal.pbio.2001855

[…] 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 […]

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