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• Ragout
  ...ple related references (complete or draft), it produces a chromosome-scale assembly (as a set of scaffolds). ...orts both small and large genomes (of mammalian scale and complexity). The assembly of highly polymorphic genomes is currently limited.
  3 KB (318 words) - 21:29, 21 August 2022
• Fast-Plast
  ...ast sequence, Fast-Plast identifies chloroplast genes present in the final assembly. .... A coverage analysis is then conducted to assess the quality of the final assembly.
  4 KB (487 words) - 21:20, 6 December 2019
• TGICL
  ...ulti-FASTA file (and an optional peer quality values file) and outputs the assembly files as produced by CAP3
  3 KB (340 words) - 20:47, 12 August 2022
• AAFTF
  [[Category:Software]][[Category:Biology]][[Category:Pipeline]][[Category:Assembly]] Automatic Assembly For The Fungi
  2 KB (245 words) - 20:45, 11 August 2022
• Hapdup
  ...is a pipeline to convert a haploid long read assembly into a dual diploid assembly. The reconstructed haplotypes preserve heterozygous structural variants (in Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin and Pavel Pevzner, "Assembly of Long Error-Prone Reads Using Repeat Graphs", Nature Biotechnology, 2019
  3 KB (324 words) - 21:07, 7 April 2022
• Hapsembler
  [[Category:Software]][[Category:Biology]][[Category:Assembly]] Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types
  3 KB (332 words) - 18:15, 15 August 2022
• LIGR
  [[Category:Software]][[Category:Biology]][[Category:Assembly]] LIGR Assembler is a sequence assembly program. It was derived from TIGR Assembler and addresses some of TIGR Asse
  2 KB (249 words) - 19:55, 15 August 2022
• Evigene
  ...ftware, combining all evidence for genes, from expressed sequences, genome assembly sequences, related species protein sequences, and any other, to annotate an
  3 KB (372 words) - 21:21, 6 December 2019
• Trans-ABySS
  De novo assembly of RNAseq data using ABySS ...th/journal/v7/n11/full/nmeth.1517.html Robertson, G., et al. 2010. De novo assembly and analysis of RNA-seq data. Nature Methods 7, 909-912(2010)]
  2 KB (260 words) - 15:39, 10 June 2022
• ATRAM
  ..., DI Huang, QC Cronk, KP Johnson. 2015\. aTRAM automated target restricted assembly method a fast method for assembling loci across divergent taxa from next-ge aTRAM does targeted ''de novo'' assembly of loci from paired-end Illumina runs and consists of the following tools:
  3 KB (350 words) - 15:23, 12 August 2022
• 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

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