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TMAP specifications

Information


Unique identifier OMICS_00694
Name TMAP
Alternative name Torrent Mapping Alignment Program
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Life Technologies
Operating system Unix/Linux
Programming languages C, C++, Javascript, Python
License GNU General Public License version 2.0
Computer skills Advanced
Version 5.4.0
Stability Stable
Maintained Yes

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Documentation


Additional information


https://github.com/iontorrent/TS/wiki

TMAP citations

 (19)
call_split

Recurrent hotspot mutations in HRAS Q61 and PI3K AKT pathway genes as drivers of breast adenomyoepitheliomas

2018
Nat Commun
PMCID: 5940840
PMID: 29739933
DOI: 10.1038/s41467-018-04128-5
call_split See protocol

[…] pth of 832× (range 560×−941×) and 664× (range 257×−949×) for the tumor and germline samples, respectively. Paired-end reads in FASTQ format were aligned to the reference human genome GRCh37 using the Torrent Mapping Alignment Program (TMAP, v3.4.1). Local realignment was performed using GATK (v3.1.1). Putative mutations were interrogated using pileup files generated with samtools mpileup (version […]

library_books

Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803

2017
Nucleic Acids Res
PMCID: 5714215
PMID: 29036481
DOI: 10.1093/nar/gkx860

[…] following the manufacturer’s instructions (). Reads were aligned against the NCBI genome sequence for Synechocystis (NC_000911.1, NC_005229.1, NC_005230.1, NC_005231.1 and NC_005232.1), applying the Torrent Mapping Alignment Program (TMAP; available from https://github.com/iontorrent/TMAP). Raw read counts were calculated using the HTSeq Python script from HTSeq-count (). The Bioconductor DESeq p […]

call_split

Exome Sequencing in a Family with Luminal Type Breast Cancer Underpinned by Variation in the Methylation Pathway

2017
Int J Mol Sci
PMCID: 5343999
PMID: 28241424
DOI: 10.3390/ijms18020467
call_split See protocol

[…] ed several intermediate steps involved in the read-processing pipeline, as illustrated in .First, sequence reads were aligned to the human reference genome (hg19) using the torrent mapping alignment (TMAP) program []. This was followed by read analysis and processing using the preinstalled Torrent Suite™ Software and variant calling with the Torrent Variant Caller (TVC) plug-in. Mapped reads were […]

library_books

Comparative Transcriptome Analysis Reveals Effects of Exogenous Hematin on Anthocyanin Biosynthesis during Strawberry Fruit Ripening

2016
Int J Genomics
PMCID: 5198259
PMID: 28074176
DOI: 10.1155/2016/6762731

[…] en removing the bases that were counted. The high-quality clean reads were mapped against the strawberry reference genome (http://strawberry-garden.kazusa.or.jp/) using Ion Torrent's mapping program (TMAP, version 0.2.3; https://github.com/iontorrent/TMAP). No more than two mismatches were allowed in the sequence alignment. Quality assessment of reads, statistics of alignment, sequencing saturatio […]

call_split

Revisiting the morbid genome of Mendelian disorders

2016
Genome Biol
PMCID: 5123336
PMID: 27884173
DOI: 10.1186/s13059-016-1102-1
call_split See protocol

[…] here particles were processed for sequencing on the Ion Proton instrument (Thermo Fisher, Carlsbad, CA, USA).After running several quality checks as described before, the reads were aligned using the tmap program (Ion Torrent Suite, Thermo Fisher, Carlsbad, CA, USA, https://github.com/iontorrent/TS) to the reference hg19 sequence. The variants within the aligned reads were called using the Torrent […]

call_split

ALK FISH patterns and the detection of ALK fusions by next generation sequencing in lung adenocarcinoma

2016
Oncotarget
PMCID: 5347743
PMID: 27769042
DOI: 10.18632/oncotarget.12705
call_split See protocol

[…] fusions and ALK 3′/5' (TK/EC domains) expression, a custom bioinformatics pipeline was used as previously described []. First, raw data in FASTQ format was aligned to a custom reference genome using TMAP [https://github.com/iontorrent/TMAP; accessed Jun 26, 2014] after adapter sequences were removed by cutadapt. FastQC [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/; accessed Jun 26, 2 […]

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