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NxTrim: optimized trimming of Illumina mate pair reads
[article]
2014
bioRxiv
pre-print
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The sequence either side of the adapter site is triaged into "virtual libraries" of mate pairs, paired-end reads and single-ended reads. ...
While "adapter trimming" is a well-studied area of bioinformatics, existing tools do not fully exploit the particular properties of NMP data and discard more data than is necessary.Results:We present NxTrim ...
NxTrim converts raw NMP reads into four "virtual libraries:" • MP: a set of known mate pairs having an outward-facing relative orientation and an EGD whose distribution mirrors the size distribution of ...
doi:10.1101/007666
fatcat:clvwz3di3bhcrb3cqemrtp6x2y
NxTrim: optimized trimming of Illumina mate pair reads: Table 1
2015
Bioinformatics
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NxTrim makes full use of the sequence on both sides of the adapter site to build 'virtual libraries' of mate pairs, paired-end reads and single-ended reads. ...
Motivation: Mate pair protocols add to the utility of paired-end sequencing by boosting the genomic distance spanned by each pair of reads, potentially allowing larger repeats to be bridged and resolved ...
Funding All authors are employees of Illumina Inc., a public company that develops and markets systems for genetic analysis, and receive shares as part of their compensation. ...
doi:10.1093/bioinformatics/btv057
pmid:25661542
fatcat:y3pfkah4ujh27k2egwaubfgoji
Extensive and deep sequencing of the Venter/HuRef genome for developing and benchmarking genome analysis tools
[article]
2018
bioRxiv
pre-print
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We prepared and sequenced 200 bp and 350 bp short-insert whole-genome sequencing libraries (sequenced to 100x and 40x genomic coverages respectively) as well as 2 kb, 5 kb, and 12 kb mate-pair libraries ...
We produced an extensive collection of deep re-sequencing datasets for the Venter/HuRef genome using the Illumina massively-parallel DNA sequencing platform. ...
Nxtrim outputs four sets of reads, 237 designated "Mate Pair", "Paired-End", "Singleton", and "Unknown." ...
doi:10.1101/281709
fatcat:ysrfkgg4ffb2zhio7zethp4tmi
Twinkle twinkle brittle star: the draft genome of {\it Ophioderma brevispinum} (Echinodermata: Ophiuroidea) as a resource for regeneration research
2022
Zenodo
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This Zenodo upload contains data from the draft genome of the brittle star Ophioderma brevispinum (Say, 1859). Please read our 'READ-ME.md' file for additional details. ...
Proposed manuscript title: "Twinkle twinkle brittle star: the draft genome of {\it Ophioderma brevispinum} (Echinodermata: Ophiuroidea) as a resource for regeneration research." ...
mostly mate pairs), paired-end, and single-end sequence reads. ...
doi:10.5281/zenodo.4247705
fatcat:57cly2aeirdxhcy2m2yacqbwlq
Extensive and deep sequencing of the Venter/HuRef genome for developing and benchmarking genome analysis tools
2018
Scientific Data
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
We prepared and sequenced 200 bp and 350 bp short-insert whole-genome sequencing libraries (sequenced to 100x and 40x genomic coverages respectively) as well as 2 kb, 5 kb, and 12 kb mate-pair libraries ...
We produced an extensive collection of deep re-sequencing datasets for the Venter/HuRef genome using the Illumina massively-parallel DNA sequencing platform. ...
Nxtrim outputs four sets of reads, designated "Mate Pair", "Paired-End", "Singleton", and "Unknown." ...
doi:10.1038/sdata.2018.261
pmid:30561434
pmcid:PMC6298255
fatcat:dcbqh5gh7zeqjifvuifamvh4qu
Hybrid de novo whole-genome assembly and annotation of the model tapeworm Hymenolepis diminuta
2019
Scientific Data
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The combination of Illumina paired-end, Illumina mate-pair and Oxford Nanopore Technology reads greatly improved the assembly of the H. diminuta genome. ...
The final genome assembly is 177 Mbp with contig N50 size of 75 kbp and a scaffold N50 size of 2.3 Mbp. ...
Table 3 . 3 NxTrim statistics.Fig. 1 MP dataset after NxTrim trimming insert size histogram. ...
doi:10.1038/s41597-019-0311-3
pmid:31796747
pmcid:PMC6890685
fatcat:6bngdg6ltfhwfdtyhi74keedxi
Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes
2017
Genome Biology and Evolution
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NxTrim utilizes the position of the junction identifier sequence in Nextera mate-pair data to classify reads of mate pair libraries as true mate pair reads, paired-end reads, or singleton reads. 1.9.2 ...
When running NxTrim, we used the "--preserve-mp" flag to prefer mate pair reads as output even if paired-end reads would be longer. ...
doi:10.1093/gbe/evx158
pmid:28992302
pmcid:PMC5629816
fatcat:nh3assj5nngmblbpf66yvmzpoa
First annotated draft genomes of non-marine ostracods (Ostracoda, Crustacea) with different reproductive modes
[article]
2020
bioRxiv
pre-print
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For genome assembly, we used an Illumina-based sequencing technology, resulting in assemblies of similar sizes for the three species (335-382Mb) and with scaffold numbers and their N50 (19-56 kb) in the ...
same orders of magnitude. ...
SM3: Estimation of genome size and heterozygosity by genome profiling analysis Raw paired-end resequencing reads were trimmed using the same strategy as described in SM2. ...
doi:10.1101/2020.12.02.409169
fatcat:zcu7p6r5tfav5kglffqqpotitm
ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter
2017
Genome Research
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We present assembly benchmarks of human Genome in a Bottle 250 bp Illumina paired-end and 6 kbp mate-pair libraries from a single individual, yielding a NG50 (NGA50) scaffold contiguity of 3.5 (3.0) Mbp ...
With ABySS 1.0, we originally showed that assembling the human genome using short 50 bp sequencing reads was possible by aggregating the half terabyte of compute memory needed over several computers using ...
The Illumina 6 kbp mate-pair sequencing data may be downloaded from https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/ AshkenazimTrio/sequence.index.AJtrio_Illumina_6kb_matepair_wgs_ ...
doi:10.1101/gr.214346.116
pmid:28232478
pmcid:PMC5411771
fatcat:64o77pmh3vb7nnkugcg7lcjw2m
ABySS 2.0: Resource-Efficient Assembly of Large Genomes using a Bloom Filter
[article]
2016
bioRxiv
pre-print
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We present assembly benchmarks of human Genome in a Bottle 250 bp Illumina paired-end and 6 kbp mate-pair libraries from a single individual, yielding a NG50 (NGA50) scaffold contiguity of 3.5 (3.0) Mbp ...
With ABySS 1.0, we originally showed that assembling the human genome using short 50 bp sequencing reads was possible by aggregating the half terabyte of compute memory needed over several computers using ...
The Illumina 6 kbp mate-pair sequencing data may be downloaded from https://github.com/genome-in-a-bottle/giab_data_indexes/blob/master/ AshkenazimTrio/sequence.index.AJtrio_Illumina_6kb_matepair_wgs_ ...
doi:10.1101/068338
fatcat:jtmknrgenbgy3gw36gfmirovte
An Annotated Chromosome-Level Reference Genome of the Red-Eared Slider Turtle (Trachemys scripta elegans)
2020
Genome Biology and Evolution
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This TSE assembly is 2.269 Gb in length, has one of the highest scaffold N50 and N90 values of any published turtle genome to date (N50=129.68 Mb and N90=19 Mb) and has a total of 28,415 annotated genes ...
Acknowledgments We acknowledge and thank the Museum of Vertebrate Zoology at University of California Berkeley and the California Academy of Sciences Herpetology Department and their staff, in particular ...
Carol Spencer (MVZ) and Lauren Scheinberg (CAS); the staff of the CAS Center for Comparative Genomics for their help with lab work; the CAS Center for Comparative Genomics' computational resources; Shawn ...
doi:10.1093/gbe/evaa063
pmid:32227195
pmcid:PMC7186784
fatcat:4zlipjpcgrhm3e22thseljn7by
First draft genome assembly of the desert locust, Schistocerca gregaria [version 2; peer review: 2 approved, 1 approved with reservations]
2021
F1000Research
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Methods: High molecular weight DNA derived from two adult males was used for Mate Pair and Paired End Illumina sequencing and PacBio sequencing. ...
Results: In total, 1,316 Gb Illumina reads and 112 Gb PacBio reads were produced and assembled. ...
Ellen De Meester and Sarah De Keulenaer from NxtGNT Belgium for their practical expertise and assistance in the Illumina sequencing experiments. ...
doi:10.12688/f1000research.25148.2
doaj:e18cc55912cc454789c269f3b68432bb
fatcat:nbjfmftd2zaxrmvgovqrckazaq
First draft genome assembly of the desert locust, Schistocerca gregaria
2020
F1000Research
Preserved Fulltext
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The file type is application/pdf.
Methods: High molecular weight DNA derived from two adult males was used for Mate Pair and Paired End Illumina sequencing and PacBio sequencing. ...
Results: In total, 1,316 Gb Illumina reads and 112 Gb PacBio reads were produced and assembled. ...
Ellen De Meester and Sarah De Keulenaer from NxtGNT Belgium for their practical expertise and assistance in the Illumina sequencing experiments. ...
doi:10.12688/f1000research.25148.1
pmid:33163158
pmcid:PMC7607483
fatcat:wofra34omjarhi4ayd25y6bkfi
De novo assembly and annotation of Asiatic lion (Panthera leo persica) genome
[article]
2019
bioRxiv
pre-print
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We report the first draft of the whole genome assembly of a male Asiatic lion, Atul and whole transcriptomes of five Asiatic lion individuals. ...
Evaluation of genetic diversity placed the Asiatic lion in the lowest bracket of genomic diversity index highlighting the gravity of its conservation status. ...
Acknowledgements We acknowledge the incessant support of the Dr. Rakesh Mishra, Director, ...
doi:10.1101/549790
fatcat:g6ytnbltpnhbjdlpgf6sgk2bim
Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi
2017
Scientific Reports
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This approach is a promising tool for reconstructing genomes of facultative symbionts, such as lichen-forming fungi, from metagenomic reads. ...
of ecological communities. ...
Some analyses were performed on the FUCHS cluster of the Center for Scientific Computing (CSC) of the Goethe University in Frankfurt am Main. ...
doi:10.1038/s41598-017-14576-6
pmid:29097759
pmcid:PMC5668418
fatcat:eelgqwihy5bqngvm3vhbbml7du
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