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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

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