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TEBreak specifications

Information


Unique identifier OMICS_13820
Name TEBreak
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Aligned sequence data and the reference genome corresponding to the alignment.
Input format BAM
Output data Insertion predictions
Output format TXT
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Stability Beta
Requirements
SAMtools, bwa, LAST, minia
Maintained Yes

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Information


Unique identifier OMICS_13820
Name TEBreak

Versioning


No version available

Documentation


TEBreak citations

 (2)
library_books

Resolving the prevalence of somatic transposition in Drosophila

2017
PMCID: 5553932
PMID: 28742021
DOI: 10.7554/eLife.28297.015

[…] the analysis of discordant read pairs in paired-end sequencing data, where one read maps onto a mobile element, and the other is used to determine the location of the insertion in the genome (e.g. tebreak [], t-lex [], retroseq [], relocate [], temp []). since we used temp in our previous study (), we used it again here. we first validated our new sequencing data and the utility of temp […]

library_books

Evidence for L1 associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme

2016
PMCID: 5105311
PMID: 27843499
DOI: 10.1186/s13100-016-0076-6

[…] were generated (additional file : table s1). rc-seq fastq files are available from the european nucleotide archive (ena) under the identifier prjeb1785.fig. 1 , rc-seq read data were analysed using tebreak (https://github.com/adamewing/tebreak/tree/f7f01c1) with settings –mincluster 2, −minclip 30, −minq 1. briefly, tebreak aligned rc-seq reads against the human reference genome (hg19) using […]


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