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- ...allows a user to bypass several standard steps, including read filtering, assembly, gene prediction, gene annotation, all vs. all comparisons, orthology predi2 KB (292 words) - 18:42, 12 July 2023
- ...ritz, A., Bremges, A., Deng, ZL. et al. Haploflow: strain-resolved de novo assembly of viral genomes. Genome Biol 22, 212 (2021)]2 KB (287 words) - 20:31, 3 January 2022
- [[Category:Assembly]]2 KB (295 words) - 17:31, 15 August 2022
- [[Category:Software]][[Category:Biology]][[Category:Assembly]]3 KB (300 words) - 14:02, 15 August 2022
- ...works applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can b2 KB (290 words) - 14:37, 21 August 2023
- ...s in FastQ format. Mapping to a whole-genome reference sequence or de novo assembly or the short reads is not necessary.2 KB (287 words) - 15:26, 21 June 2023
- [[Category:Software]][[Category:assembly]]2 KB (284 words) - 21:14, 20 November 2023
- HapCompass implements a novel HAPCOMPASS algorithm for haplotype assembly of densely sequenced human genome data. The algorithm operates on a graph w2 KB (287 words) - 18:13, 15 August 2022
- ...e novo assembler for PacBio and Oxford Nanopore (ONT) data. It produces an assembly from all-vs-all raw read alignments without an error correction stage. It a2 KB (296 words) - 21:24, 6 December 2019
- ...gnificantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.2 KB (297 words) - 16:44, 15 August 2022
- ...290925 Dierckxsens N., Mardulyn P. and Smits G. (2016) NOVOPlasty: De novo assembly of organelle genomes from whole genome data. Nucleic Acids Research, doi: 13 KB (310 words) - 21:23, 6 December 2019
- ...sequencing reads. stringMLST predicts the ST of an isolate in a completely assembly and alignment free manner. The tool is designed in a light-weight, platform2 KB (292 words) - 20:45, 12 August 2022
- |{{#vardefine:url|https://support.10xgenomics.com/de-novo-assembly/software/}} Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library3 KB (306 words) - 16:55, 10 June 2022
- ...ces a new graph binning algorithm and achieves the best haplotype-resolved assembly given trio data.3 KB (303 words) - 22:23, 27 August 2020
- ...ific use cases: 1) to robustly estimate the base accuracy of CCS reads and assembly contigs, and 2) to investigate the systematic error rate of CCS reads. It a2 KB (293 words) - 16:10, 10 March 2021
- Multi-sample de novo assembly and variant calling using Linked de bruijn graphs. Variant calling with and3 KB (297 words) - 22:22, 8 September 2020
- ...are generated independently when all binning tools are applied to the same assembly.3 KB (315 words) - 21:21, 6 December 2019
- YASRA (Yet Another Short Read Assembler) performs comparative assembly of short reads using a reference genome, which can differ substantially fro3 KB (304 words) - 20:56, 12 August 2022
- ...ise, which is presented as low-quality bases, has serious impact on genome assembly and mapping. We propose SeqyClean, a specialized cleaning pipeline that all3 KB (312 words) - 22:41, 21 August 2022
- ...assemblies for the same isolate, Trycycler can combine them into a single assembly that is better than any of your inputs.3 KB (305 words) - 18:13, 22 July 2021
- ...s without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl geno3 KB (310 words) - 17:44, 22 August 2022
- title={Recycler: an algorithm for detecting plasmids from de novo assembly graphs},3 KB (297 words) - 14:21, 11 October 2022
- ...rom minimap2) and detects five different variant classes between the query assembly and the reference: deletions, insertions, tandem and interspersed duplicati3 KB (306 words) - 17:16, 31 May 2022
- Corset is a command-line program to go from a de novo transcriptome assembly to gene-level counts. Our software takes a set of reads that have been mult3 KB (309 words) - 17:09, 10 June 2022
- ...t requires a set of target transcripts (either from a reference or de-novo assembly) to quantify. All you need to run Salmon is a FASTA file containing your re3 KB (305 words) - 19:29, 3 June 2022
- [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:Assembly]]2 KB (313 words) - 20:42, 18 August 2022
- HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires lo3 KB (315 words) - 19:53, 17 August 2020
- ...l-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does3 KB (306 words) - 20:10, 18 August 2022
- [[Category:Software]][[Category:Biology]][[Category:Assembly]][[Category:Genomics]]2 KB (297 words) - 19:41, 21 August 2022
- ...create a new processed sequence file as output. This design encourages the assembly of the seq_crumbs utilities with Unix pipes to create complex pipelines. Th3 KB (328 words) - 15:12, 27 May 2022
- ...peats directly from sequence reads. It based on the idea of frequent k-mer assembly. REPdenovo provides many functionalities, and can generate much longer repe3 KB (327 words) - 21:43, 21 August 2022
- ...), but requires significantly less computing resources and storages. After assembly, the per-base accuracy is about 98-99.8%, to further improve single base ac3 KB (312 words) - 18:03, 10 May 2021
- ntEdit is a scalable genomics application for polishing genome assembly drafts. ntEdit simplifies polishing and "haploidization" of gene and genome3 KB (316 words) - 21:23, 6 December 2019
- IVA: accurate de novo assembly of RNA virus genomes.2 KB (300 words) - 16:06, 7 December 2021
- ...r the representation of de Bruijn graphs are important for genome sequence assembly. A fully dynamic data structure supporting efficient and exact membership q3 KB (312 words) - 21:20, 6 December 2019
- ...ta, profiled from solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining re3 KB (314 words) - 20:12, 8 February 2021
- ...present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other3 KB (321 words) - 17:25, 10 June 2022
- ...n Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS ONE 9(11): e112963. doi:10.1371/journal.pone.0112963]3 KB (321 words) - 20:23, 12 August 2022
- ...zov YB, Campbell EM, Switzer WM, Skums P, Mangul S, Zelikovsky A. Accurate assembly of minority viral haplotypes from next-generation sequencing through effici3 KB (301 words) - 20:24, 1 May 2024
- ...ced with 'N' symbols. Occasionally, if the genome is in the early stage of assembly the non-masked sequences are too short for most reference indexes to be bui2 KB (361 words) - 20:30, 12 August 2022
- [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Assembly]]3 KB (326 words) - 14:41, 15 August 2022
- ...an unbiased manner an estimation of genome completeness of a fungal genome assembly. The strategy is based on the screening of the genome using a set of highly3 KB (326 words) - 21:20, 6 December 2019
- Zhang, X. Zhang, S. Zhao, Q. Ming, R. Tang, H. Assembly of allele-aware, chromosomal scale autopolyploid genomes based on Hi-C data3 KB (299 words) - 12:35, 12 August 2022
- De novo assembly is a commonly used application of next-generation sequencing experiments. T3 KB (331 words) - 16:52, 15 August 2022
- ...mes to perform comparative evolutionary studies. It post-processes de novo assembly transcripts into putative coding sequences and their corresponding amino ac3 KB (331 words) - 13:29, 4 October 2021
- ...ly/2016/03/09/bioinformatics.btw064 Sahlin K, Chikhi R, Arvestad L (2016) "Assembly scaffolding with PE-contaminated mate-pair libraries." Bioinformatics]3 KB (332 words) - 12:51, 15 August 2022
- ...-graph based assembler Velvet modified and extended for de novo metagenome assembly. The fundamental ideas are first decomposing de Bruijn graph constructed fr3 KB (326 words) - 19:28, 18 August 2022
- ...E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T, “Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads”. Ge3 KB (318 words) - 21:23, 6 December 2019
- MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Lay3 KB (340 words) - 18:24, 18 August 2022
- ...Oxford Nanopore, etc.) or preassembled contigs to fill N-gap in the genome assembly.3 KB (321 words) - 15:35, 20 April 2021
- ..., Borodina T, Himmelbauer H SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Research 2007 17: 1697-1703 KB (313 words) - 22:42, 21 August 2022
- ...linakge maps or chromosomal-scale pseudomolecules combining de novo genome assembly and genetic mapping. The method assumes availability of genome-wide genotyp3 KB (344 words) - 13:45, 3 November 2020
- JASPER (Jellyfish based Assembly Sequence Polisher for Error Reduction) is an efficient polishing tool for d3 KB (354 words) - 16:42, 14 December 2023
- ..., Berlin K, Miller JR, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research. (2017)3 KB (358 words) - 14:26, 14 April 2020
- ...olds to reconstruct chromosomes is an essential step during de novo genome assembly. This process is often assisted by various mapping techniques. Because each3 KB (361 words) - 21:11, 6 December 2019
- ...boundaries between long DNA sequences. It can be useful for mapping genome assembly or long reads (PacBio/ONT) to reference genome(s). Given a minimum alignmen3 KB (359 words) - 17:28, 27 May 2022
- ...the k-mer error correction framework, first introduced by the EULER genome assembly package. Unlike EULER and similar progams, Quake utilizes a robust mixture3 KB (367 words) - 18:50, 10 June 2022
- ...the basic arithmetic type, by using fast algorithms, with highly optimised assembly code for the most common inner loops for a lot of CPUs, and by a general em3 KB (373 words) - 13:43, 3 June 2022
- ...ance evaluation results, in terms of correction quality and de novo genome assembly measures, reveal that Musket is consistently one of the top performing subs3 KB (351 words) - 13:44, 19 August 2022
- sequences, such as those generated by de novo RNA-Seq transcript assembly3 KB (371 words) - 16:54, 22 August 2022
- HAplotype and PHylodynamics pipeline for viral assembly, population genetics, and phylodynamics.3 KB (405 words) - 16:40, 14 March 2023
- ...ove accuracy and provide read-backed phasing, adaptively selecting between assembly and a faster alignment-based haplotyping approach at each variant locus. Th3 KB (369 words) - 14:24, 10 October 2023
- ...ttp://www.sciencemag.org/cgi/content/abstract/287/5461/2196 A Whole-Genome Assembly of Drosophila]. Science 287 2196-2204.3 KB (375 words) - 20:55, 12 August 2022
- ...map it. Liftoff can also find additional gene copies present in the target assembly that are not annotated in the reference.3 KB (399 words) - 13:14, 23 September 2020
- ...tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), an3 KB (412 words) - 22:31, 8 September 2020
- * aplCal3 - ''A. californica'' 3.0 WGS assembly, 4331 contigs * GRCh38.p11 - Human Genome assembly GRCh38.p117 KB (975 words) - 18:52, 10 April 2024
- * If no assembly data is available, chewieSnake can assemble reads into draft genomes using4 KB (457 words) - 15:02, 23 October 2023
- ...ext-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART was used as a primary tool for3 KB (440 words) - 21:10, 6 December 2019
- ...enomes - sequences can be assembled into contigs. QDD3 does NOT do de novo assembly, but can take contigs (scaffolds/chormosomes) as an input, and extracts mic4 KB (485 words) - 20:08, 21 August 2022
- assembly. BLAT has several major stages. It uses the index to find regions in3 KB (484 words) - 13:03, 15 August 2022
- * The assembly of raw read data to contigs4 KB (517 words) - 18:23, 21 August 2022
- ...hakottil G., Mapleson D.L., Swarbreck D. Leveraging multiple transcriptome assembly methods for improved gene structure annotation. GigaScience, Volume 7, Issu4 KB (495 words) - 19:45, 18 August 2022
- ...Barr, A. Jusufi, S. Sanders, M. L. Klein, and A. Z. Panagiotopoulos. Self-assembly of coarse-grained ionic surfactants accelerated by graphics processing unit5 KB (607 words) - 15:40, 6 June 2022