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• SEQuel
  ...contain a substantial number of errors that need to be corrected after the assembly process. The algorithm behind SEQuel makes use of a graph structure called
  3 KB (382 words) - 22:39, 21 August 2022
• Maq
  Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences.
  3 KB (377 words) - 19:47, 12 August 2022
• Tigmint
  ...inked reads from 10x Genomics Chromium. The reads are first aligned to the assembly, and the extents of the large DNA molecules are inferred from the alignment ...rg Bohlmann, Steven J.M. Jones and Inanc Birol (2018). Tigmint: correcting assembly errors using linked reads from large molecules. BMC Bioinformatics, 19(1).]
  3 KB (370 words) - 21:29, 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
• FALCON
  Falcon: a set of tools for fast aligning long reads for consensus and assembly ...kit is a set of simple code collection which I use for studying efficient assembly algorithm for haploid and diploid genomes. It has some back-end code implem
  3 KB (395 words) - 15:19, 15 August 2022
• SRAssembler
  ...mbler repository is the distribution point of our code for selective local assembly of genomic regions matching a homologous query protein or DNA sequence. ...Chou, and Volker P. Brendel (2018) SRAssembler: Selective Recursive local Assembly of homologous genomic regions.]
  3 KB (381 words) - 15:33, 27 May 2022
• MEGAHIT
  ...oil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG c ...HIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics, doi: 10.1093/bioinformatics/b
  3 KB (367 words) - 18:31, 18 August 2022
• GRIDSS
  ...based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence. ...specific genomic rearrangement detection using positional de Bruijn graph assembly. Genome Research, 2017 doi: 10.1101/gr.222109.117]
  3 KB (388 words) - 21:20, 6 December 2019
• Wengan
  identifies miss-assemblies at different steps of the assembly process. For more information ...., Buena-Atienza, E., Ossowski, S. and Sagot,M-F. Efficient hybrid de novo assembly of human genomes with WENGAN. Nature Biotechnology (2020),
  4 KB (472 words) - 20:55, 12 August 2022
• PsiCLASS
  ...robust with the aggregation method used, including the built-in voting and assembly-based approaches such as StringTie-merge and TACO. Therefore, it can be eff ...nd Florea, L. A multi-sample approach increases the accuracy of transcript assembly. Nat Commun 10, 5000 (2019)]
  4 KB (480 words) - 15:00, 14 December 2022
• TACO
  TACO: Multi-sample transcriptome assembly from RNA-Seq
  2 KB (234 words) - 18:53, 1 June 2022
• RACA
  RACA: Reference-Assisted Chromosome Assembly
  2 KB (235 words) - 19:45, 10 June 2022
• BUSCO
  BUSCO stands for Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Ortholo BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
  5 KB (607 words) - 19:38, 27 March 2023
• FRAMA
  Description: a transcriptome assembly and mRNA annotation pipeline
  2 KB (236 words) - 21:21, 6 December 2019
• Ipyrad
  ipyrad, an interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, d
  2 KB (239 words) - 19:00, 15 August 2022
• MetaBCC-LR
  ...bly helps to enhance the assembly quality while significantly reducing the assembly cost in terms of time and memory usage. The efficiency and accuracy of Meta
  6 KB (774 words) - 14:28, 15 December 2022
• Assemblytics
  Assemblytics: a web analytics tool for the detection of variants from an assembly
  2 KB (252 words) - 17:02, 29 September 2020
• 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
• Clview
  Clview is an nteractive tool for inspecting the ACE format assembly files generated by CAP3 or phrap.
  2 KB (252 words) - 13:48, 15 August 2022

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