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• 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
• DISCOVAR de novo
  [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Assembly]] DISCOVAR is a new variant caller and DISCOVAR de novo a new genome assembler, both designed for state-of-the-art data. Their inpu
  3 KB (326 words) - 14:41, 15 August 2022
• GapFiller
  De novo assembly is a commonly used application of next-generation sequencing experiments. T
  3 KB (331 words) - 16:52, 15 August 2022
• PlantTribes
  ...mes to perform comparative evolutionary studies. It post-processes de novo assembly transcripts into putative coding sequences and their corresponding amino ac
  3 KB (331 words) - 13:29, 4 October 2021
• Wengan
  identifies miss-assemblies at different steps of the assembly process. For more information ...., Buena-Atienza, E., Ossowski, S. and Sagot,M-F. Efficient hybrid de novo assembly of human genomes with WENGAN. Nature Biotechnology (2020),
  4 KB (472 words) - 20:55, 12 August 2022
• PolyGembler
  ...linakge maps or chromosomal-scale pseudomolecules combining de novo genome assembly and genetic mapping. The method assumes availability of genome-wide genotyp
  3 KB (344 words) - 13:45, 3 November 2020
• ALLMAPS
  ...olds to reconstruct chromosomes is an essential step during de novo genome assembly. This process is often assisted by various mapping techniques. Because each
  3 KB (361 words) - 21:11, 6 December 2019
• Musket
  ...ance evaluation results, in terms of correction quality and de novo genome assembly measures, reveal that Musket is consistently one of the top performing subs
  3 KB (351 words) - 13:44, 19 August 2022
• TransDecoder
  sequences, such as those generated by de novo RNA-Seq transcript assembly
  3 KB (371 words) - 16:54, 22 August 2022
• Wgs
  ...r is scientific software for biological research. Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler. It reconstructs long seq ...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
• ART
  ...ext-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART was used as a primary tool for
  3 KB (440 words) - 21:10, 6 December 2019
• QDD
  ...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 mic
  4 KB (485 words) - 20:08, 21 August 2022

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