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• Xander
  ...ruijn graphs and protein HMMs. The inclusion of HMM information guides the assembly, with concomitant gene annotation. .... Xander: Employing a Novel Method for Efficient Gene-Targeted Metagenomic Assembly. Microbiome.2015, 3:32. DOI: 10.1186/s40168-015-0093-6.]
  3 KB (381 words) - 19:07, 10 June 2022
• Zorro
  ...3Mb to 100Mb. The main feature of Zorro is the treatment before and after assembly to avoid errors.
  2 KB (284 words) - 17:54, 22 August 2022
• FALCON unzip
  ...icBiosciences/FALCON/wiki/FALCON-FALCON-Unzip-%22For-Phased-Diploid-Genome-Assembly-with-Single-Molecule-Real-Time-Sequencing%22
  3 KB (302 words) - 18:53, 12 August 2022
• FastPlast
  ...ast sequence, Fast-Plast identifies chloroplast genes present in the final assembly.
  2 KB (288 words) - 20:23, 23 May 2022
• Triobinning
  Programs implementing the trio-binning genome assembly method Koren et al. (2018). "Complete assembly of parental haplotypes with trio binning." Nature Biotechnology 2018/10/22/
  2 KB (276 words) - 13:31, 15 August 2022
• Newbler
  [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Assembly]][[Category:De Novo]] Newbler is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the
  2 KB (305 words) - 16:17, 19 August 2022
• Assembly-stats
  |{{#vardefine:app|assembly-stats}} |{{#vardefine:url|https://github.com/sanger-pathogens/assembly-stats}}
  2 KB (293 words) - 14:56, 12 August 2022
• Clover
  [[Category:Assembly]] k-mers.Clover achieves a superior assembly quality in terms of corrected
  2 KB (296 words) - 13:47, 15 August 2022
• DEXTRACTOR
  assembly and reconstruction from the source .bax.h5 HDF5 files produced by the PacBi to produce a highly accurate consensus sequence as the last step in the assembly
  3 KB (441 words) - 19:20, 10 June 2022
• HAPCUT
  [[Category:Software]][[Category:Biology]][[Category:Assembly]] HapCUT is a max-cut based algorithm for haplotype assembly that uses the mix of sequenced fragments from the two chromosomes of an ind
  2 KB (298 words) - 18:13, 15 August 2022
• Platypus
  ...Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb. It has been extensively tested on whole ...um, Andrew O. M. Wilkie, Gil McVean, Gerton Lunter. Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing
  3 KB (435 words) - 19:21, 10 June 2022
• ARC
  ...and a set of semi-similar reference targets is available to initialize the assembly process.
  3 KB (430 words) - 14:32, 12 August 2022
• Merqury
  Often, genome assembly projects have illumina whole genome sequencing reads available for the asse The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference. Merqury provides a se
  3 KB (306 words) - 13:54, 12 August 2020
• Stringtie
  ...lgorithmic techniques from de novo genome assembly to help with transcript assembly. Its input can include not only the spliced read alignments used by referen
  3 KB (301 words) - 20:45, 12 August 2022
• Oases
  [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Assembly]] the absence of any genomic assembly. It was developed by Marcel Schulz (MPI
  2 KB (293 words) - 17:25, 19 August 2022
• CAP3
  [[Category:Software]][[Category:Biology]][[Category:Assembly]] CAP3 is a sequence assembly program.
  2 KB (302 words) - 13:19, 15 August 2022
• Flye
  ...nce. The package also includes a polisher module, which produces the final assembly of high nucleotide-level quality.
  3 KB (317 words) - 21:20, 6 December 2019
• Quickmerge
  ...For more details, please see the paper that describes it. Citation for ONP assembly merging coming soon!
  3 KB (325 words) - 21:24, 6 December 2019
• Captus
  ...ation Sequencing) data. Captus was initially designed specifically for the assembly of target-enriched (e.g. via hybridization of RNA or DNA probes) sequencing
  3 KB (321 words) - 16:36, 16 November 2022
• HLAminer
  ...geted assembly of short sequence reads (HPTASR), performs targeted de novo assembly of HLA NGS reads and align the resulting contigs to reference HLA alleles f ...d, the read is recruited as a candidate for de novo assembly. Upon de novo assembly of all recruited reads, a set of contigs is generated. Only sequence contig
  4 KB (541 words) - 14:55, 14 December 2022

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