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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
• PurgeDups
  Purge haplotigs and overlaps in an assembly based on read depth
  2 KB (257 words) - 18:50, 27 May 2022
• Rainbow
  clustering and de novo assembly.
  2 KB (254 words) - 21:24, 6 December 2019
• Staden
  A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX
  2 KB (254 words) - 15:59, 22 August 2022
• Skmer
  ...mes from low-coverage sequencing reads (genome-skims), without needing any assembly or alignment step.
  2 KB (260 words) - 13:31, 15 August 2022
• WhatsHap
  ...ts using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short r
  2 KB (269 words) - 21:29, 6 December 2019
• JCVI
  ...libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.
  2 KB (265 words) - 14:30, 4 September 2020
• Yagcloser
  [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:Assembly]]
  2 KB (265 words) - 19:07, 1 April 2024
• RagTag
  Fast reference-guided genome assembly scaffolding
  2 KB (263 words) - 15:27, 13 August 2020
• Pbipa
  ...ved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi reads to produce h
  2 KB (268 words) - 21:58, 27 April 2022
• Fast-gep
  ...r high-resolution genealogical relationship of bacterial isolates with WGS assembly data.
  2 KB (283 words) - 15:46, 22 July 2022
• 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

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