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• 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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