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• 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
• Shovill
  ...uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assem
  2 KB (286 words) - 18:13, 23 August 2022
• FALCON fc run cfg
  # The length cutoff used for seed reads usef for pre-assembly
  2 KB (248 words) - 20:31, 2 August 2021
• 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
• GROCSVs
  ...eline for identifying large-scale structural variants, performing sequence assembly at the breakpoints, and reconstructing the complex structural variants usin
  2 KB (274 words) - 21:21, 6 December 2019
• PhyloFlash
  ...KB Seah, Elmar Pruesse. phyloFlash — Rapid SSU rRNA profiling and targeted assembly from metagenomes.]
  2 KB (279 words) - 00:09, 29 October 2020
• BRIG
  ...arisons between a large number of genomes, with a focus on handling genome assembly data.
  2 KB (278 words) - 16:25, 10 June 2022
• RaGOO
  A tool to order and orient genome assembly contigs via Minimap2 alignments to a reference genome.
  2 KB (280 words) - 21:24, 6 December 2019
• 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
• FALCON fc large run cfg
  # The length cutoff used for seed reads usef for pre-assembly
  2 KB (266 words) - 20:30, 2 August 2021
• Read2tree
  ...allows a user to bypass several standard steps, including read filtering, assembly, gene prediction, gene annotation, all vs. all comparisons, orthology predi
  2 KB (292 words) - 18:42, 12 July 2023
• 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
• SCOP
  [[Category:Assembly]]
  2 KB (295 words) - 17:31, 15 August 2022
• Crass
  [[Category:Software]][[Category:Biology]][[Category:Assembly]]
  3 KB (300 words) - 14:02, 15 August 2022
• Medaka
  ...works applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can b
  2 KB (290 words) - 14:37, 21 August 2023
• 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]]
  2 KB (284 words) - 21:14, 20 November 2023
• HapCompass
  HapCompass implements a novel HAPCOMPASS algorithm for haplotype assembly of densely sequenced human genome data. The algorithm operates on a graph w
  2 KB (287 words) - 18:13, 15 August 2022
• 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
• FLASh
  ...gnificantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.
  2 KB (297 words) - 16:44, 15 August 2022
• 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
• 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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