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• 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
• 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
• DISCOVAR de novo
  [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Assembly]]
  3 KB (326 words) - 14:41, 15 August 2022
• FGMP
  ...an unbiased manner an estimation of genome completeness of a fungal genome assembly. The strategy is based on the screening of the genome using a set of highly
  3 KB (326 words) - 21:20, 6 December 2019
• Allhic
  Zhang, X. Zhang, S. Zhao, Q. Ming, R. Tang, H. Assembly of allele-aware, chromosomal scale autopolyploid genomes based on Hi-C data
  3 KB (299 words) - 12:35, 12 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
• BESST
  ...ly/2016/03/09/bioinformatics.btw064 Sahlin K, Chikhi R, Arvestad L (2016) "Assembly scaffolding with PE-contaminated mate-pair libraries." Bioinformatics]
  3 KB (332 words) - 12:51, 15 August 2022
• MetaVelvet
  ...-graph based assembler Velvet modified and extended for de novo metagenome assembly. The fundamental ideas are first decomposing de Bruijn graph constructed fr
  3 KB (326 words) - 19:28, 18 August 2022
• Platanus
  ...E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T, “Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads”. Ge
  3 KB (318 words) - 21:23, 6 December 2019
• MaSuRCA
  MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Lay
  3 KB (340 words) - 18:24, 18 August 2022
• TGSGapCloser
  ...Oxford Nanopore, etc.) or preassembled contigs to fill N-gap in the genome assembly.
  3 KB (321 words) - 15:35, 20 April 2021
• SHARCGS
  ..., Borodina T, Himmelbauer H SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Research 2007 17: 1697-170
  3 KB (313 words) - 22:42, 21 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
• Jasper
  JASPER (Jellyfish based Assembly Sequence Polisher for Error Reduction) is an efficient polishing tool for d
  3 KB (354 words) - 16:42, 14 December 2023
• Canu
  ..., Berlin K, Miller JR, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research. (2017)
  3 KB (358 words) - 14:26, 14 April 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
• MasHmap
  ...boundaries between long DNA sequences. It can be useful for mapping genome assembly or long reads (PacBio/ONT) to reference genome(s). Given a minimum alignmen
  3 KB (359 words) - 17:28, 27 May 2022
• Quake
  ...the k-mer error correction framework, first introduced by the EULER genome assembly package. Unlike EULER and similar progams, Quake utilizes a robust mixture
  3 KB (367 words) - 18:50, 10 June 2022
• GMP
  ...the basic arithmetic type, by using fast algorithms, with highly optimised assembly code for the most common inner loops for a lot of CPUs, and by a general em
  3 KB (373 words) - 13:43, 3 June 2022
• 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
• Haphpipe
  HAplotype and PHylodynamics pipeline for viral assembly, population genetics, and phylodynamics.
  3 KB (405 words) - 16:40, 14 March 2023
• Strelka
  ...ove accuracy and provide read-backed phasing, adaptively selecting between assembly and a faster alignment-based haplotyping approach at each variant locus. Th
  3 KB (369 words) - 14:24, 10 October 2023
• Wgs
  ...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
• Liftoff
  ...map it. Liftoff can also find additional gene copies present in the target assembly that are not annotated in the reference.
  3 KB (399 words) - 13:14, 23 September 2020
• MetaWRAP
  ...tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), an
  3 KB (412 words) - 22:31, 8 September 2020
• BLASTDB
  * aplCal3 - ''A. californica'' 3.0 WGS assembly, 4331 contigs * ​GRCh38.p11 - Human Genome assembly ​GRCh38.p11
  7 KB (975 words) - 18:52, 10 April 2024
• Chewiesnake
  * If no assembly data is available, chewieSnake can assemble reads into draft genomes using
  4 KB (457 words) - 15:02, 23 October 2023
• 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
• BLAT
  assembly. BLAT has several major stages. It uses the index to find regions in
  3 KB (484 words) - 13:03, 15 August 2022
• Phyluce
  * The assembly of raw read data to contigs
  4 KB (517 words) - 18:23, 21 August 2022
• Mikado
  ...hakottil G., Mapleson D.L., Swarbreck D. Leveraging multiple transcriptome assembly methods for improved gene structure annotation. GigaScience, Volume 7, Issu
  4 KB (495 words) - 19:45, 18 August 2022
• HOOMD
  ...Barr, A. Jusufi, S. Sanders, M. L. Klein, and A. Z. Panagiotopoulos. Self-assembly of coarse-grained ionic surfactants accelerated by graphics processing unit
  5 KB (607 words) - 15:40, 6 June 2022

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