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• 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
• 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
  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
• NtEdit
  ntEdit is a scalable genomics application for polishing genome assembly drafts. ntEdit simplifies polishing and "haploidization" of gene and genome
  3 KB (316 words) - 21:23, 6 December 2019
• IVA
  IVA: accurate de novo assembly of RNA virus genomes.
  2 KB (300 words) - 16:06, 7 December 2021
• DynamicDBG
  ...r the representation of de Bruijn graphs are important for genome sequence assembly. A fully dynamic data structure supporting efficient and exact membership q
  3 KB (312 words) - 21:20, 6 December 2019
• 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
• PILON
  ...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
• Cliquesnv
  ...zov YB, Campbell EM, Switzer WM, Skums P, Mangul S, Zelikovsky A. Accurate assembly of minority viral haplotypes from next-generation sequencing through effici
  3 KB (301 words) - 20:24, 1 May 2024
• Reference Indexes
  ...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 bui
  2 KB (361 words) - 20:30, 12 August 2022

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