Sambamba: fast processing of NGS alignment formats

Тарасов, А. В.; Vilella, Albert J.; Cuppen, Edwin; Nijman, Isaäc J.; Prins, Pjotr

doi:10.1093/bioinformatics/btv098

Cited by 1,819 publications

(1,362 citation statements)

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“…Trimmed reads were aligned to the human genome (hg19) using Bowtie v2.2.9 (Langmead and Salzberg, 2012) with parameter -X 2000 to ensure that long fragments were able to align. Properly paired alignments in a 20-Mb region of chromosome 8 (chr8:120000000-140000000) were extracted, and duplicate fragments were removed from this set using Sambamba (Tarasov et al, 2015). To identify nucleosome positions, fragments were processed as described by Buenrostro et al (2013): fragments of length 180–247 bp were considered to be one nucleosome, and fragments of length 315–473 bp were considered to be two nucleosomes and split into two fragments.…”

Section: Star Methodsmentioning

confidence: 99%

Global Inhibition with Specific Activation: How p53 and MYC Redistribute the Transcriptome in the DNA Double-Strand Break Response

et al. 2017

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Summary In response to stresses, cells often halt normal cellular processes; yet stress-specific pathways must bypass such inhibition to generate effective responses. We investigated how cells redistribute global transcriptional activity in response to DNA damage. We show that oscillatory increase of p53 levels in response to double-strand breaks drives counter-oscillatory decrease of MYC levels. Using RNA-seq of newly synthesized transcripts, we found that p53-mediated reduction of MYC suppressed general transcription, with the most highly expressed transcripts reduced to a greater extent. In contrast, upregulation of p53 targets was relatively unaffected by MYC suppression. Reducing MYC during the DNA damage response was important for cell fate regulation, as counteracting MYC repression reduced cell cycle arrest and elevated apoptosis. Our study shows that “global inhibition with specific activation” of transcriptional pathways is important for the proper response to DNA damage, and this mechanism may be a general principle used in many stress responses.

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Section: Star Methodsmentioning

confidence: 99%

Global Inhibition with Specific Activation: How p53 and MYC Redistribute the Transcriptome in the DNA Double-Strand Break Response

et al. 2017

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“…We then optimized the alignments according to GATK (version 3.6) MuTect2 (27) best practices. We used sambamba (28) to sort and index the alignments, Picard MarkDuplicates (http://broadinstitute. github.io/picard) to identify duplicate artifacts, and GATK BaseRecalibrator with knownSites set to dbSNP .…”

Section: Methodsmentioning

confidence: 99%

Mutational profiles of breast cancer metastases from a rapid autopsy series reveal multiple evolutionary trajectories

Avigdor¹,

Cimino‐Mathews²,

DeMarzo³

et al. 2017

JCI Insight

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“…Duplicates were marked with Picard Tools MarkDuplicates v0.1.111 (http://picard.sourceforge.net). All alignment manipulations, including sorting and indexing, was performed with sambamba v0.4.6 [18]. Alignment quality was assessed using Picard Tools, Samtools v1.0 and BamTools v2.2.2 [19,20].…”

Section: Methodsmentioning

confidence: 99%

Mutated Huntingtin Causes Testicular Pathology in Transgenic Minipig Boars

Macakova

Bohuslavová²,

Vochozková³

et al. 2016

Neurodegener Dis

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Background: Huntington's disease is induced by CAG expansion in a single gene coding the huntingtin protein. The mutated huntingtin (mtHtt) primarily causes degeneration of neurons in the brain, but it also affects peripheral tissues, including testes. Objective: We studied sperm and testes of transgenic boars expressing the N-terminal region of human mtHtt. Methods: In this study, measures of reproductive parameters and electron microscopy (EM) images of spermatozoa and testes of transgenic (TgHD) and wild-type (WT) boars of F1 (24-48 months old) and F2 (12-36 months old) generations were compared. In addition, immunofluorescence, immunohistochemistry, Western blot, hormonal analysis and whole-genome sequencing were done in order to elucidate the effects of mtHtt. Results: Evidence for fertility failure of both TgHD generations was observed at the age of 13 months. Reproductive parameters declined and progressively worsened with age. EM revealed numerous pathological features in sperm tails and in testicular epithelium from 24- and 36-month-old TgHD boars. Moreover, immunohistochemistry confirmed significantly lower proliferation activity of spermatogonia in transgenic testes. mtHtt was highly expressed in spermatozoa and testes of TgHD boars and localized in all cells of seminiferous tubules. Levels of fertility-related hormones did not differ in TgHD and WT siblings. Genome analysis confirmed that insertion of the lentiviral construct did not interrupt any coding sequence in the pig genome. Conclusions: The sperm and testicular degeneration of TgHD boars is caused by gain-of-function of the highly expressed mtHtt.

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Sambamba: fast processing of NGS alignment formats

Cited by 1,819 publications

References 9 publications

Global Inhibition with Specific Activation: How p53 and MYC Redistribute the Transcriptome in the DNA Double-Strand Break Response

Global Inhibition with Specific Activation: How p53 and MYC Redistribute the Transcriptome in the DNA Double-Strand Break Response

Mutational profiles of breast cancer metastases from a rapid autopsy series reveal multiple evolutionary trajectories

Mutated Huntingtin Causes Testicular Pathology in Transgenic Minipig Boars

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