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opencc-by-4.0May 2019View details →

Genome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication: insertion data and derivative models

This data repository provides access to the LINE-1 (L1) insertion site data from Flasch, et al., 2019: <a href="https://www.sciencedirect.com/science/article/pii/S0092867419302338?via%3Dihub">https://www.sciencedirect.com/science/article/pii/S0092867419302338?via%3Dihub</a> Please see file L1_actual_and_random_insertions_help.docx for more detailed information. Files weighted_model_142_102917_corrected.txt and weighted_model_142_102917_uncorrected.txt carry a list of all possible 7-mer insertion sites, one per row, with site weights calculated based on observed L1 insertion sites. The files are either corrected or uncorrected for the frequency of those sites as found in the human genome, respectively. A header line defines the columns. The weight files described above were used to construct the simulated hg19 insertions sets described below. Archive all_insertion_sets.tar contains a series of insertion files, each with the complete data set used to analyze insertions from the named cell line. Column 5 is the iteration number, where: <ul> <li>iteration == 0 identifies the actual, observed insertions</li> <li>each iteration > 0 identifies one round of simulation, up to 10K total simulations</li> <li>each iteration has the same number of insertions</li> </ul> Column 4 is the insertion number within each actual or simulated insertion set. Please see the companion Zenodo data set: 10.5281/zenodo.12538130 for more information about creating insertion site models from your own insertion data.

opencc-by-4.0May 2019View details →

Genome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication: creating new models

This data repository provides code and general instructions for creating new LINE-1 (L1) insertion site models as described in Flasch, et al., 2019: <a href="https://www.sciencedirect.com/science/article/pii/S0092867419302338?via%3Dihub">https://www.sciencedirect.com/science/article/pii/S0092867419302338?via%3Dihub</a> Please see file L1_Simulation_Files_help.docx for more detailed information. File L1Simulation_filelist.xlsx lists the files described in the Word file and found in L1Simulations.tar.gz. Required large file ChrmsALL_table_sortEN.bed.gz is found individually. Importantly, like the paper analysis, this file is specific to the hg19 version of the human genome. Please see the companion Zenodo data set 10.5281/zenodo.8233858 if you only want to access our insertion data and the resulting models we created.

opencc-by-4.0Feb 2019View details →

Supplementary data and scripts for Willemsen et al., 2019 "Genome plasticity in Papillomaviruses and de novo emergence of E5 oncogenes"

Supplementary data for Willemsen et al., 2019 "Genome plasticity in Papillomaviruses and de novo emergence of E5 oncogenes". The data set consists of three folders: “Alignments”, “Bali-Phy” and “RandomPermutationTests”. The “Alignments” folder contains the different alignments used for phylogenetic tree construction and comparison. The “Bali-Phy” folder contains the final results and convergence diagnostics of the Common Ancestry tests obtained by using the Bali-Phy software. The “RandomPermutationTests” folder contains all the data and scripts to repeat the random permutation tests described in the manuscript. Please see the corresponding README files for more information.

opencc-by-4.0Jul 2019View details →

De novo genome assembly of the meadow brown butterfly, Maniola jurtina

1. Whole-genome GFF file (raw and filtered for min. gene length) [Maniola.jurtina.gff3, Maniola_jurtina_filtered.gff3] 2. List of M. jurtina proteins [Mjurtina_proteins.fa]. 3. Results of spot pattern genes BLAST against M. jurtina proteome [Lepidoptera_MJ_protein_matches.xlsx].  4. Annotations [blast2go_export.txt]

opencc-by-4.0Sep 2024View details →

Genome-wide tool for rapid de novo identification and visualisation of interspersed and tandem

Genomic repeats are functionally ubiquitous structural units found in all genomes. Studying these repeats of different origins is essential for the evolution and adaptation of a given organism. These repeating patterns have manifold signatures and structures with varying degrees of homology, making their identification challenging. To address this challenge, we developed a new algorithm and software that can rapidly and accurately detect any repeated sequences de novo with varying degrees of homology in genomic sequences in interspersed or clustered repeats. Numerous forms of repeated sequences and complex patterns can be identified, even for complex sequence variants and implicit or mixed types of repeat blocks. Direct and inverted-repeat elements, perfect and imperfect microsatellite repeats, and any short- or long-tandem repeat belonging to a wide range of higher-order repeat structures of telomers or large satellite sequences can be detected. By combining precision and versatility, our tool contributes significantly to elucidating the intricate landscape of genomic repeats.

opencc-by-4.0Aug 2023View details →

Draft de novo genome assemblies of a male and female Amphibolurus muricatus (jacky dragon)

Four de novo nuclear genome assemblies of Amphibolurus muricatus Assembly 1.0: A 10x Genomics linked-read sequencing assembly • AmpMurF_1.0.fa.tar.gz (female A. muricatus) • AmpMurM_1.0.fa.tar.gz (male A. muricatus) Assembly 1.1: Further scaffolding of assembly 1.0 using RNA-seq data • AmpMurF_1.1.fa.tar.gz (female A. muricatus) • AmpMurM_1.1.fa.tar.gz (male A. muricatus) Assembly 2.0: Further scaffolding of assembly 1.0 using SLR-superscaffolder • AmpMurF_2.0.fa.tar.gz (female A. muricatus) • AmpMurM_2.0.fa.tar.gz (male A. muricatus) Assembly 3.0: An stLFR linked-read sequencing assembly • AmpMurF_3.0.fa.tar.gz (female A. muricatus) • AmpMurM_3.0.fa.tar.gz (male A. muricatus) Methods Assembly 1.0: A 10x Genomics linked-read sequencing assembly Male and female A. muricatus genome sequencing libraries were constructed on the Chromium system (10x Genomics, Pleasanton, CA, USA) by the Ramaciotti Centre for Genomics (Sydney, Australia). The Chromium instrument enables unique barcoding of long stretches of DNA on gel beads. The barcodes allow later reconstruction of long DNA fragments from a series of short DNA fragments with the same barcode (i.e., linked-reads). After barcoding, DNA was sheared into smaller fragments and sequenced on the NovaSeq 6000 platform (Illumina, CA, USA) to generate 151 bp paired-end (PE) reads. A total of 904.9 M raw 10x Genomics Chromium linked-reads were generated. Raw 10x data were assembled with Supernova v2.1.1 (Weisenfeld et al., 2017) and a FASTA file was generated using the ‘pseudohap style’ option in Supernova mkoutput. All female (~450 M) and male (~550 M) read pairs were utilised (female sequencing depth ca 50.3×; male, ca 47.8×). The resulting assemblies was further scaffolded with ARKS v1.0.3 (Coombe et al., 2018), reusing the 10x reads, and the companion LINKS program (v1.8.7) (Warren et al., 2015). ARKS employs a k-mer approach to map linked barcodes to the contigs in the initial Supernova assembly to generate a scaffold graph with estimated distances for LINKS input. These assemblies were denoted AmpMurF_1.0 (female) and AmpMurM_1.0 (male). We used GapCloser v1.12 (part of SOAPdenovo2) (Luo et al., 2012) to fill gaps in the assembly. GapCloser was run using the parameter -l 150) and clean 10x Genomics reads PE reads.   Assembly 1.1: Further scaffolding using RNA-seq data We attempted to improve the v1.0 genome assemblies’ contiguity using RNA-sequencing reads. RNA-seq reads (from brain, ovary, and testis; see below) were filtered (i.e., cleaned) to remove adapters and low-quality reads using Flexbar v3.4.0 and used to further re-scaffold the v1.0 assemblies (FASTA files before gapclosing) with P_RNA_scaffolder (Zhu et al., 2018). The default Flexbar settings discards all reads with any uncalled bases. A final round of scaffolding was performed on the resulting assemblies using L_RNA_scaffolder (Xue et al., 2013). These assemblies were denoted AmpMurF_1.1 (female) and AmpMurM_1.1 (male). As before, GapCloser and clean 10x Genomics reads were used to fill gaps.      Assembly 2.0: Further scaffolding using SLR-superscaffolder As an alternative approach, we attempted to improve the v1.0 genome assemblies’ contiguity using SLR-superscaffolder (Guo et al., 2021). Briefly, SLR-superscaffolder employs single tube long fragment read (stLFR) sequencing (Wang et al., 2019) reads (see section below) to generate hybrid genome assemblies. The software was run with default parameters except for PE_SEED_MIN=300 (minimum contig size to fill; default 1000). These assemblies were denoted AmpMurF_2.0 (female) and AmpMurM_2.0 (male). GapCloser and clean stLFR reads (with the barcode removed using https://github.com/BGI-Qingdao/stLFR_barcode_split) were used to fill gaps.      Assembly 3.0: An stLFR linked-read sequencing and supernova assembly We also generated independent assemblies for the individuals sequenced on the 10x Genomics Chromium system using single tube long fragment read (stLFR) sequencing (Wang et al., 2019). BGI (Brisbane, Australia) generated ~100×-coverage 100-bp paired-end reads (plus a 42-bp stLFR barcode on the right/_2 read). Low-quality reads, PCR duplicates, and adaptors were removed using SOAPnuke v1.5 (Chen et al. 2018). The stLFRdenovo pipeline (<a href="https://github.com/BGI-biotools/stLFRdenovo">https://github.com/BGI-biotools/stLFRdenovo</a>), which is based on Supernova and customized for stLFR data, was used to generate a de novo genome assembly. The stLFRdenovo tool ‘FillGaps’ was used to fill gaps. References Chen, Y., Chen, Y., Shi, C., Huang, Z., Zhang, Y., Li, S., Li, Y., Ye, J., Yu, C., Li, Z., et al. (2018). SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience 7, 1-6. Coombe, L., Zhang, J., Vandervalk, B.P., Chu, J., Jackman, S.D., Birol, I., and Warren, R.L. (2018). ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers. BMC Bioinformatics 19, 234. Guo, L., Xu, M., Wang, W., Gu, S., Zhao, X., Chen, F., Wang, O., Xu, X., Seim, I., Fan, G., et al. (2021). SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme. BMC Bioinformatics 22, 158. Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y., et al. (2012). SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1, 18. Wang, O., Chin, R., Cheng, X., Wu, M.K.Y., Mao, Q., Tang, J., Sun, Y., Anderson, E., Lam, H.K., Chen, D., et al. (2019). Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly. Genome Res 29, 798-808. Warren, R.L., Yang, C., Vandervalk, B.P., Behsaz, B., Lagman, A., Jones, S.J., and Birol, I. (2015). LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads. Gigascience 4, 35. Weisenfeld, N.I., Kumar, V., Shah, P., Church, D.M., and Jaffe, D.B. (2017). Direct determination of diploid genome sequences. Genome Res 27, 757-767. Xue, W., Li, J.T., Zhu, Y.P., Hou, G.Y., Kong, X.F., Kuang, Y.Y., and Sun, X.W. (2013). L_RNA_scaffolder: scaffolding genomes with transcripts. BMC Genomics 14, 604. Zhu, B.H., Xiao, J., Xue, W., Xu, G.C., Sun, M.Y., and Li, J.T. (2018). P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads. BMC Genomics 19, 175.

opencc-by-4.0Feb 2020View details →

Dataset for "Whole-genome de novo assemblies reveal structural variations and organelle-to-nucleus DNA transfers in Asian and African rice""

DXCWR_O.rufipogon_scaffolded_anchored.fa.gz --Scaffolded and anchored genome assembly for O. rufipogon  DXCWR. DXCWR_O.rufipogon_scaffolded_anchored.gff.gz --Gene annotation for the genome assembly DXCWR_O.rufipogon_scaffolded_anchored.fa. DXCWR_O.rufipogon_scaffolded_anchored_repeatmasker.gff.gz --Repeat annotation for the genome assembly DXCWR_O.rufipogon_scaffolded_anchored.fa. IRGC104165_O.glaberrima_scaffolded_anchored.fa.gz --Scaffolded and anchored genome assembly for O. glaberrima  IRGC104165. IRGC104165_O.glaberrima_scaffolded_anchored.gff.gz --Gene annotation for the genome assembly IRGC104165_O.glaberrima_scaffolded_anchored.fa. IRGC104165_O.glaberrima_scaffolded_anchored_repeatmasker.gff.gz --Repeat annotation for the genome assembly IRGC104165_O.glaberrima_scaffolded_anchored.fa. W1411_O.barthii_scaffolded_anchored.fa.gz --Scaffolded and anchored genome assembly for O. barthii  W1411. W1411_O.barthii_scaffolded_anchored.gff.gz --Gene annotation for the genome assembly W1411_O.barthii_scaffolded_anchored.fa. W1411_O.barthii_scaffolded_anchored_repeatmasker.gff.gz --Repeat annotation for the genome assembly W1411_O.barthii_scaffolded_anchored.fa. W2014_O.nivara_scaffolded_anchored.fa.gz --Scaffolded and anchored genome assembly for O. nivara  W2014. W2014_O.nivara_scaffolded_anchored.gff.gz --Gene annotation for the genome assembly  W2014_O.nivara_scaffolded_anchored.fa. W2014_O.nivara_scaffolded_anchored_repeatmasker.gff.gz --Repeat annotation for the genome assembly  W2014_O.nivara_scaffolded_anchored.fa.

opencc-zeroJun 2021View details →

Draft de novo genome assembly of the elusive jaguarundi, Puma yagouaroundi

The Puma lineage within the family Felidae consists of three species that last shared a common ancestor around 4.9 million years ago. Whole-genome sequences of two species from the lineage were previously reported: the cheetah (Acinonyx jubatus) and the mountain lion (Puma concolor). The present report describes a whole-genome assembly of the remaining species, the jaguarundi (Puma yagouaroundi). We sequenced the genome of a male jaguarundi with 10X Genomics linked reads and assembled the whole-genome sequence. The assembled genome contains a series of scaffolds that reach the length of chromosome arms and is similar in scaffold contiguity to the genome assemblies of cheetah and puma, with a contig N50 = 100.2 kbp and a scaffold N50 = 49.27 Mbp. We assessed the assembled sequence of the jaguarundi genome using BUSCO, aligned reads of the sequenced individual and another published female jaguarundi to the assembled genome, annotated protein-coding genes, repeats, genomic variants and their effects with respect to the protein-coding genes, and analyzed differences of the two jaguarundis from the reference mitochondrial genome. The jaguarundi genome assembly and its annotation were compared in quality, variants and features to the previously reported genome assemblies of puma and cheetah. Computational analyzes used in the study were implemented in transparent and reproducible way to allow their further reuse and modification.

opencc-by-4.0Nov 2023View details →

PacBio HiFi de-novo assembled genome and mitochondrial genome for Orbicella faveolata

Final assembly using Funannotate of Orbicella faveolata from PacBio HiFi reads. For full methods please see the publication.

opencc-by-4.0Dec 2018View details →

De novo whole genome assembly of the giant tiger prawn (Penaeus monodon) from Vietnam

Basecalled Nanopore FastQ files for the Vietnamese giant tiger prawn and its genome assemblies. FastQ files (LSK109 sample prep sequenced on a MinION device for 48 hours). Read stats are in *_stat.txt: TP_A.fastq : gDNA was extracted using Zymo quick DNA minikit from ethanol-preserved muscle tissue TP_B.fastq : Same as TP_A.fastq TP_C.fastq : gDNA was extracted using conventional salting out method (longer read length but reduced yield) Assemblies: v1_MaSuRCA.fasta: Assembly using poly-G trimmed Illumina reads v2_NanoporeScaf.fasta : Scaffolding with Nanopore long reads v3_RNA_NanoporeScaf.fasta: Scaffolding of v2 with RNA reads v4_NCBI_Filt.fasta: post NCBI contaminant and carry-over adapter removal (final version) Annotation: Braker2_annotation.gff3.gz: Inititial Braker2 gff3 output Braker2_CDS.fna.gz: Initial Braker2 predicted genes Braker2_prot.faa.gz: Protein translation of Braker2_CDS.fna CAZy.tar.gz: CAZy annotation for four crustacean species Filtered_Gene.tar.gz: List of genes with functional annotation and/or orthologs Interproscan_result.tsv: Raw InterProScan output OrthoFinder2.tar.gz: OrthoFinder2 output. Proteins used to infer orthologs are included as ".faa".

opencc-by-4.0Dec 2013View details →

Figure 3 in De novo mutations in the genome organizer CTCF cause intellectual disability

Figure 3. - Principal component analysis (PCA) of morphometric data. The ellipse highlights the group formed by the albino and normally pigmented specimens of the same size class. The albino is represented by the white square. Squares (N3 = 20-30 cm size-class); inverse triangles (N4 = 30-40 cm), circles (N5 = 40-50 cm), lozenges (N6 = 50-60 cm), and triangles (N7 = 60-70 cm).

opencc-by-4.0Dec 2013View details →

Figure 2 in De novo mutations in the genome organizer CTCF cause intellectual disability

Figure 2. - Regressions of log of disc width vs. log of weight (A) and log of total length vs. log of weight (B) using the albino specimen and data from 28 female individuals of G. micrura. The albino specimen is represented by the white dot.

opencc-zeroMay 2020View details →

Data from: A de novo chromosome-level genome assembly of Coregonus sp. "Balchen": one representative of the Swiss Alpine whitefish radiation

Salmonids are of particular interest to evolutionary biologists due to their incredible diversity of life-history strategies and the speed at which many salmonid species have diversified. In Switzerland alone, over 30 species of Alpine whitefish from the subfamily Coregoninae have evolved since the last glacial maximum, with species exhibiting a diverse range of morphological and behavioural phenotypes. This, combined with the whole genome duplication which occurred in the ancestor of all salmonids, makes the Alpine whitefish radiation a particularly interesting system in which to study the genetic basis of adaptation and speciation and the impacts of ploidy changes and subsequent rediploidization on genome evolution. Although well curated genome assemblies exist for many species within Salmonidae, genomic resources for the subfamily Coregoninae are lacking. To assemble a whitefish reference genome, we carried out PacBio sequencing from one wild-caught Coregonus sp. "Balchen" from Lake Thun to ~90x coverage. PacBio reads were assembled independently using three different assemblers, Falcon, Canu and wtdbg2 and subsequently scaffolded with additional Hi-C data. All three assemblies were highly contiguous, had strong synteny to a previously published Coregonuslinkage map, and when mapping additional short-read data to each of the assemblies, coverage was fairly even across most chromosome-scale scaffolds. Here, we present the first de novogenome assembly for the Salmonid subfamily Coregoninae. The final 2.2 Gb wtdbg2 assembly included 40 scaffolds, an N50 of 51.9 Mb, and was 93.3% complete for BUSCOs. The assembly consisted of ~52% TEs and contained 44,525 genes.

opencc-by-4.0Jan 2023View details →

Baseline assemblies for "ntLink: a toolkit for de novo genome assembly scaffolding and mapping using long reads" protocol

ntLink is a flexible de novo genome scaffolding toolkit which can be run in various modes depending on the desired user output, with multiple new functionalities recently introduced. Here, we provide the baseline assembly datasets used in the ntLink protocol paper "ntLink: a toolkit for de novo genome assembly scaffolding and mapping using long reads". The provided assemblies are ABySS (short-read) and Flye (long-read) assemblies of Caenorhabditis elegans genome sequencing data. The ABySS (v2.1.4) assembly utilized paired-end short reads (accession DRR008444), and was run with the following parameters: k=64 l=40 s=1000 q=15 B=10G j=8 kc=3 H=4 S=1000-10000 N=9.The C. elegans Flye (v2.5) assembly was run using Oxford Nanopore long reads (accession SRR10028109) and the following parameters: --nano-raw SRR10028109.fastq -g100m -t48.

opencc-by-4.0Mar 2023View details →

De novo assembly of a long-read Amblyomma americanum genome

Genome assemblies of Amblyomma americanum generated from PacBio HiFi sequencing of 50 individual female ticks. This repository contains the unphased diploid assembly generated by the Flye assembler (Arcadia_Amblyomma_americanum_asm001.fasta). In addition, there are two associated fasta files containing sequences generated by submitting the unphased diploid assembly to separation by the Purge_Dups pipeline (purged pseudo-haploid assembly and haplotig assembly). Flye assembler: https://github.com/fenderglass/Flye Purge_Dups pipeline: https://github.com/dfguan/purge_dups NCBI Bioproject: PRJNA932813

opencc-by-4.0Mar 2023View details →

De novo assembly of a long-read Amblyomma americanum genome (NCBI/Genbank deposited genome)

Genome assembly of Amblyomma americanum generated from PacBio HiFi sequencing of 50 individual female ticks. This repository contains the phased pseudo-haploid tick genome generated after assembly using Flye, phasing using Purge_Dups, and clean-up using custom python scripts generated in-house.  NCBI Bioproject: PRJNA932813

opencc-by-4.0Apr 2023View details →

Assemblies for "Linear time complexity de novo long read genome assembly with GoldRush"

GoldRush is a de novo genome assembly algorithm with linear time complexity in the number of input long sequencing reads. We tested GoldRush on Oxford Nanopore Technologies datasets with different base error profiles describing the genomes of three human cell lines (NA24385, HG01243 and HG02055), Oryza sativa (rice), and Solanum lycopersicum (tomato). Here, we provide the assemblies for the GoldRush, Flye, Redbean and Shasta assemblies of these long read datasets.

publicOct 2024View details →

Data from: De novo reference genome of a Geomyid rodent, Botta’s pocket gopher (Thomomys bottae)

Open the record for dataset details and reuse information.