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• NOVOPlasty
  ...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
• StringMLST
  ...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, platform
  2 KB (292 words) - 20:45, 12 August 2022
• 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
• YAK
  ...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 a
  2 KB (293 words) - 16:10, 10 March 2021
• Mccortex
  Multi-sample de novo assembly and variant calling using Linked de bruijn graphs. Variant calling with and
  3 KB (297 words) - 22:22, 8 September 2020
• DASTool
  ...are generated independently when all binning tools are applied to the same assembly.
  3 KB (315 words) - 21:21, 6 December 2019
• YASRA
  YASRA (Yet Another Short Read Assembler) performs comparative assembly of short reads using a reference genome, which can differ substantially fro
  3 KB (304 words) - 20:56, 12 August 2022
• SeqyClean
  ...ise, which is presented as low-quality bases, has serious impact on genome assembly and mapping. We propose SeqyClean, a specialized cleaning pipeline that all
  3 KB (312 words) - 22:41, 21 August 2022
• Trycycler
  ...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
• 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
• Svim-asm
  ...rom minimap2) and detects five different variant classes between the query assembly and the reference: deletions, insertions, tandem and interspersed duplicati
  3 KB (306 words) - 17:16, 31 May 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
• MIRA
  [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:Assembly]]
  2 KB (313 words) - 20:42, 18 August 2022
• HASLR
  HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires lo
  3 KB (315 words) - 19:53, 17 August 2020
• 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
• Prokka
  [[Category:Software]][[Category:Biology]][[Category:Assembly]][[Category:Genomics]]
  2 KB (297 words) - 19:41, 21 August 2022
• Seq crumbs
  ...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. Th
  3 KB (328 words) - 15:12, 27 May 2022

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