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Reference genome assemblies
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Metagenome sampling bias for geographical location and lifestyle is partially responsible for the incomplete catalog of reference genomes of gut microbial species. Thus, genome assembly from currently underrepresented populations may effectively expand the reference gut microbiome and improve taxonomic and functional profiling.
20p
vibransone
28-03-2024
5
2
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In this paper we present IntroMap, a bioinformatics pipeline for the screening of candidate plants through the application of signal processing techniques to NGS data, using alignment to a reference genome sequence (annotation is not required) that shares homology with the recurrent parental cultivar, and without the need for de novo assembly of the read data or variant calling.
12p
vinarcissa
21-03-2023
6
1
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The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by applying low-pass sequencing and recovering whole organelle genomes computationally.
20p
vigalileogalilei
27-02-2022
14
1
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There is growing interest in using genetic variants to augment the reference genome into a graph genome, with alternative sequences, to improve read alignment accuracy and reduce allelic bias. While adding a variant has the positive effect of removing an undesirable alignment score penalty, it also increases both the ambiguity of the reference genome and the cost of storing and querying the genome index.
16p
vigalileogalilei
27-02-2022
10
1
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The human reference genome is still incomplete, especially for those population-specific or individual-specific regions, which may have important functions. Here, we developed a HUman Pan-genome ANalysis (HUPAN) system to build the human pan-genome.
11p
vielonmusk
30-01-2022
10
0
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We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in minutes. After the pseudomolecules are constructed, RaGOO identifies structural variants, including those spanning sequencing gaps.
17p
vielonmusk
30-01-2022
5
0
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RNA sequencing using the latest single-molecule sequencing instruments produces reads that are thousands of nucleotides long. The ability to assemble these long reads can greatly improve the sensitivity of long-read analyses. Here we present StringTie2, a reference-guided transcriptome assembler that works with both short and long reads.
13p
vielonmusk
30-01-2022
9
0
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Most gene prediction methods detect coding sequences from transcriptome assemblies in the absence of closely related reference genomes. Such methods are of limited application due to high transcript fragmentation and extensive assembly errors, which may lead to redundant or false coding sequence predictions.
12p
vialfrednobel
29-01-2022
13
0
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Evolutionary origins of derived morphologies ultimately stem from changes in protein structure, gene regulation, and gene content. A well-assembled, annotated reference genome is a central resource for pursuing these molecular phenomena underlying phenotypic evolution.
23p
vialfrednobel
29-01-2022
8
2
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The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies.
30p
viarchimedes
26-01-2022
11
0
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Haplotype-aware diploid genome assembly is crucial in genomics, precision medicine, and many other disciplines. Long-read sequencing technologies have greatly improved genome assembly. However, current long-read assemblers are either reference based, so introduce biases, or fail to capture the haplotype diversity of diploid genomes.
26p
viarchimedes
26-01-2022
10
0
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Long-read de novo genome assembly continues to advance rapidly. However, there is a lack of effective tools to accurately evaluate the assembly results, especially for structural errors. We present Inspector, a reference-free long-read de novo assembly evaluator which faithfully reports types of errors and their precise locations
21p
viarchimedes
26-01-2022
10
1
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The current bovine genomic reference sequence was assembled from a Hereford cow. The resulting linear assembly lacks diversity because it does not contain allelic variation, a drawback of linear references that causes reference allele bias.
27p
viarchimedes
26-01-2022
6
0
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Recent long-read assemblies often exceed the quality and completeness of available reference genomes, making validation challenging. Here we present Merqury, a novel tool for reference-free assembly evaluation based on efficient k-mer set operations.
27p
viarchimedes
26-01-2022
14
0
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Our assembly-free linkage analysis pipeline (AFLAP) identifies segregating markers as k-mers in the raw reads without using a reference genome assembly for calling variants and provides genotype tables for the construction of unbiased, high-density genetic maps without a genome assembly.
26p
viarchimedes
26-01-2022
16
0
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Genetic maps have been fundamental to building our understanding of disease genetics and evolutionary processes. The gametes of an individual contain all of the information required to perform a de novo chromosome-scale assembly of an individual’s genome, which historically has been performed with populations and pedigrees.
19p
viarchimedes
26-01-2022
9
0
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The circum-basmati group of cultivated Asian rice (Oryza sativa) contains many iconic varieties and is widespread in the Indian subcontinent. Despite its economic and cultural importance, a high-quality reference genome is currently lacking, and the group’s evolutionary history is not fully resolved.
27p
viarchimedes
26-01-2022
12
0
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Epigenomic studies that use next generation sequencing experiments typically rely on the alignment of reads to a reference sequence. However, because of genetic diversity and the diploid nature of the human genome, we hypothesize that using a generic reference could lead to incorrectly mapped reads and bias downstream results.
22p
viarchimedes
26-01-2022
11
0
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Thousands of experiments and studies use the human reference genome as a resource each year. This single reference genome, GRCh38, is a mosaic created from a small number of individuals, representing a very small sample of the human population.
18p
viarchimedes
26-01-2022
14
0
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Salmonid fishes exhibit high levels of phenotypic and ecological variation and are thus ideal model systems for studying evolutionary processes of adaptive divergence and speciation. Furthermore, salmonids are of major interest in fisheries, aquaculture, and conservation research. Improving understanding of the genetic mechanisms underlying traits in these species would significantly progress research in these fields.
17p
vilarryellison
29-10-2021
13
1
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