Search results

• Transrate
  [[Category:Software]][[Category:Biology]][[Category:Assembly]] ...ntigs from an assembly, and help decide when to stop trying to improve the assembly.
  3 KB (316 words) - 16:54, 22 August 2022
• MECAT
  ...aligners and error correction tools. MECAT can be used for effectively de novo assemblying large genomes. ...Han, Feng Luo, Zhi Xie. MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads. Nature Methods, 2017, 14: 1072-1074]
  3 KB (324 words) - 18:29, 18 August 2022
• Trans-ABySS
  De novo assembly of RNAseq data using ABySS ...th/journal/v7/n11/full/nmeth.1517.html Robertson, G., et al. 2010. De novo assembly and analysis of RNA-seq data. Nature Methods 7, 909-912(2010)]
  2 KB (260 words) - 15:39, 10 June 2022
• Newbler
  ...re]][[Category:Biology]][[Category:NGS]][[Category:Assembly]][[Category:De Novo]] Newbler is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the
  2 KB (305 words) - 16:17, 19 August 2022
• Stringtie
  ...reference-based assemblers, but also longer contigs that were assembled de novo from unambiguous, non-branching parts of a transcript.
  3 KB (301 words) - 20:45, 12 August 2022
• MetaVelvet
  Velvet is a de novo genomic assembler specially designed for short read sequencing technologies ...ividual sub-graphs and second building scaffolds based on every decomposed de Bruijn sub-graph as isolate species genome.
  3 KB (326 words) - 19:28, 18 August 2022
• Necklace
  ...notation. Necklace is a software pipeline to run genome-guided and de novo assembly and combine the resulting transcriptomes with reference genome annotations.
  3 KB (312 words) - 21:22, 6 December 2019
• 3d-dna
  ...the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. ...hamim, M.S., Machol, I., Lander, E.S., Aiden, A.P., et al. (2017). De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.
  3 KB (328 words) - 17:51, 10 June 2022
• ABruijn
  ...ts of raw reads. This coarse sequence is then polished into a high quality assembly. ...with 50x coverage takes less than an hour on a modern desktop, while yeast assembly takes about 5 hours. A eukaryotic genome of size 200 Mbp can be assembled w
  3 KB (354 words) - 20:09, 24 August 2022
• Fast-Plast
  ...ast sequence, Fast-Plast identifies chloroplast genes present in the final assembly. .... A coverage analysis is then conducted to assess the quality of the final assembly.
  4 KB (487 words) - 21:20, 6 December 2019
• HLAminer
  ...geted assembly of short sequence reads (HPTASR), performs targeted de novo assembly of HLA NGS reads and align the resulting contigs to reference HLA alleles f ...d, the read is recruited as a candidate for de novo assembly. Upon de novo assembly of all recruited reads, a set of contigs is generated. Only sequence contig
  4 KB (541 words) - 14:55, 14 December 2022
• NOVOPlasty
  NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. ...290925 Dierckxsens N., Mardulyn P. and Smits G. (2016) NOVOPlasty: De novo assembly of organelle genomes from whole genome data. Nucleic Acids Research, doi: 1
  3 KB (310 words) - 21:23, 6 December 2019
• ARC
  ...and a set of semi-similar reference targets is available to initialize the assembly process.
  3 KB (430 words) - 14:32, 12 August 2022
• Clover
  [[Category:Assembly]] Clover is a clustering-oriented de novo assembler for Illumina sequences,
  2 KB (296 words) - 13:47, 15 August 2022
• IVA
  IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, IVA: accurate de novo assembly of RNA virus genomes.
  2 KB (300 words) - 16:06, 7 December 2021
• IAssembler
  [[Category:Software]][[Category:Biology]][[Category:Assembly]] ...y in EST assembly than other existing assemblers by employing an iterative assembly strategy and automated error corrections of mis-assemblies.
  3 KB (301 words) - 18:39, 15 August 2022
• Platanus
  Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of ...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”. Ge
  3 KB (318 words) - 21:23, 6 December 2019
• SHARCGS
  [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:De Novo]] |{{#vardefine:url|http://sharcgs.molgen.mpg.de/index.shtml}}
  3 KB (313 words) - 22:42, 21 August 2022
• Mccortex
  Multi-sample de novo assembly and variant calling using Linked de bruijn graphs. Variant calling with and without a reference genome. Between ...le/34/15/2556/4938484 Integrating long-range connectivity information into de Bruijn graphs Turner I, Garimella K, Iqbal Z, McVean G (Bioinformatics) (Ad
  3 KB (297 words) - 22:22, 8 September 2020
• Minia
  GATB-Minia-Pipeline is a de novo assembly pipeline for Illumina data. It can assemble genomes and metagenomes. * Minia 3 (contigs assembly) based on the BCALM2 (unitigs assembly) tool
  2 KB (285 words) - 13:31, 15 August 2022
• Aquamis
  AQUAMIS is a pipeline for routine assembly and quality assessment of microbial isolate sequencing experiments. It is b * shovill (based on Spades) for de-novo assembly
  3 KB (348 words) - 22:07, 20 October 2023
• GetOrganelle
  ...Li. 2018. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. bioRxiv, 256479.]
  2 KB (275 words) - 21:21, 6 December 2019
• FastPlast
  ...ast sequence, Fast-Plast identifies chloroplast genes present in the final assembly.
  2 KB (288 words) - 20:23, 23 May 2022
• Oases
  [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Assembly]] Oases is a de novo transcriptome assembler designed to produce transcripts
  2 KB (293 words) - 17:25, 19 August 2022
• Flye
  ...nce. The package also includes a polisher module, which produces the final assembly of high nucleotide-level quality.
  3 KB (317 words) - 21:20, 6 December 2019
• Evigene
  ...ftware, combining all evidence for genes, from expressed sequences, genome assembly sequences, related species protein sequences, and any other, to annotate an
  3 KB (372 words) - 21:21, 6 December 2019
• ATRAM
  ..., DI Huang, QC Cronk, KP Johnson. 2015\. aTRAM automated target restricted assembly method a fast method for assembling loci across divergent taxa from next-ge aTRAM does targeted ''de novo'' assembly of loci from paired-end Illumina runs and consists of the following tools:
  3 KB (350 words) - 15:23, 12 August 2022
• Inspector
  Inspector is a tool for assembly evaluation with long read data. The input includes a contig file, long read ...-02527-4 Chen, Y., Zhang, Y., Wang, A.Y. et al. Accurate long-read de novo assembly evaluation with Inspector. Genome Biol 22, 312 (2021).]
  3 KB (319 words) - 18:50, 15 August 2022
• SOAPdenovo
  ...enovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble
  2 KB (314 words) - 00:05, 22 August 2022
• Asset
  ...acbio, 10X, Bionano, HiC) to accumulate the support evidence for a de novo assembly.
  2 KB (253 words) - 20:07, 15 June 2023
• NECAT
  NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.
  2 KB (250 words) - 13:32, 23 June 2020
• Rainbow
  clustering and de novo assembly.
  2 KB (254 words) - 21:24, 6 December 2019
• VirusDetect
  ...s to the known virus reference database (GenBank gbvrl) as well as de novo assembly using Velvet with automated parameter optimization. The assembled contigs a
  3 KB (377 words) - 23:22, 30 July 2020
• DRAP
  Short read RNASeq de novo assembly is a well established method to study transcription of organisms lacking a
  2 KB (280 words) - 21:20, 6 December 2019
• PRICE
  ...es from such complex datasets, and it is also being applied to the de novo assembly of large individual genomes.
  2 KB (286 words) - 16:26, 10 June 2022
• Haploflow
  ...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
• Kvarq
  ...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
• Raven
  [[Category:Software]][[Category:assembly]] Raven is a de novo genome assembler for long uncorrected reads.
  2 KB (284 words) - 21:14, 20 November 2023
• SMARTdenovo
  ...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 a
  2 KB (296 words) - 21:24, 6 December 2019
• Supernova
  |{{#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 library
  3 KB (306 words) - 16:55, 10 June 2022
• Hifiasm
  ...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
• Wtdbg
  ...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 geno
  3 KB (310 words) - 17:44, 22 August 2022
• Recycler
  title={Recycler: an algorithm for detecting plasmids from de novo assembly graphs},
  3 KB (297 words) - 14:21, 11 October 2022
• Corset
  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 mult
  3 KB (309 words) - 17:09, 10 June 2022
• Salmon
  ...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 re
  3 KB (305 words) - 19:29, 3 June 2022
• Miniasm
  ...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 does
  3 KB (306 words) - 20:10, 18 August 2022
• REPdenovo
  ...peats directly from sequence reads. It based on the idea of frequent k-mer assembly. REPdenovo provides many functionalities, and can generate much longer repe ...e.0150719 Chong Chu, Rasmus Nielsen and Yufeng Wu, REPdenovo: Inferring de novo repeat motifs from short sequence reads, PLoS One 11.3 (2016): e0150719.]
  3 KB (327 words) - 21:43, 21 August 2022
• NextDenovo
  ...), but requires significantly less computing resources and storages. After assembly, the per-base accuracy is about 98-99.8%, to further improve single base ac
  3 KB (312 words) - 18:03, 10 May 2021
• TRUST4
  ...ta, profiled from solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining re
  3 KB (314 words) - 20:12, 8 February 2021
• GMcloser
  ...present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other
  3 KB (321 words) - 17:25, 10 June 2022

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