Search results

• Transrate
  [[Category:Software]][[Category:Biology]][[Category:Assembly]] ...ntigs from an assembly, and help decide when to stop trying to improve the assembly.
  3 KB (316 words) - 16:54, 22 August 2022
• MECAT
  ...aligners and error correction tools. MECAT can be used for effectively de novo assemblying large genomes. ...Han, Feng Luo, Zhi Xie. MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads. Nature Methods, 2017, 14: 1072-1074]
  3 KB (324 words) - 18:29, 18 August 2022
• 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
• Newbler
  ...re]][[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
• Stringtie
  ...reference-based assemblers, but also longer contigs that were assembled de novo from unambiguous, non-branching parts of a transcript.
  3 KB (301 words) - 20:45, 12 August 2022
• MetaVelvet
  Velvet is a de novo genomic assembler specially designed for short read sequencing technologies ...ividual sub-graphs and second building scaffolds based on every decomposed de Bruijn sub-graph as isolate species genome.
  3 KB (326 words) - 19:28, 18 August 2022
• Necklace
  ...notation. Necklace is a software pipeline to run genome-guided and de novo assembly and combine the resulting transcriptomes with reference genome annotations.
  3 KB (312 words) - 21:22, 6 December 2019
• 3d-dna
  ...the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. ...hamim, M.S., Machol, I., Lander, E.S., Aiden, A.P., et al. (2017). De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.
  3 KB (328 words) - 17:51, 10 June 2022
• ABruijn
  ...ts of raw reads. This coarse sequence is then polished into a high quality assembly. ...with 50x coverage takes less than an hour on a modern desktop, while yeast assembly takes about 5 hours. A eukaryotic genome of size 200 Mbp can be assembled w
  3 KB (354 words) - 20:09, 24 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
• 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
• NOVOPlasty
  NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. ...290925 Dierckxsens N., Mardulyn P. and Smits G. (2016) NOVOPlasty: De novo assembly of organelle genomes from whole genome data. Nucleic Acids Research, doi: 1
  3 KB (310 words) - 21:23, 6 December 2019
• 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
• Clover
  [[Category:Assembly]] Clover is a clustering-oriented de novo assembler for Illumina sequences,
  2 KB (296 words) - 13:47, 15 August 2022
• IVA
  IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, IVA: accurate de novo assembly of RNA virus genomes.
  2 KB (300 words) - 16:06, 7 December 2021
• IAssembler
  [[Category:Software]][[Category:Biology]][[Category:Assembly]] ...y in EST assembly than other existing assemblers by employing an iterative assembly strategy and automated error corrections of mis-assemblies.
  3 KB (301 words) - 18:39, 15 August 2022
• Platanus
  Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of ...E, Maruyama H, Kohara Y, Fujiyama A, Hayashi T, Itoh T, “Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads”. Ge
  3 KB (318 words) - 21:23, 6 December 2019
• SHARCGS
  [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:De Novo]] |{{#vardefine:url|http://sharcgs.molgen.mpg.de/index.shtml}}
  3 KB (313 words) - 22:42, 21 August 2022
• Mccortex
  Multi-sample de novo assembly and variant calling using Linked de bruijn graphs. Variant calling with and without a reference genome. Between ...le/34/15/2556/4938484 Integrating long-range connectivity information into de Bruijn graphs Turner I, Garimella K, Iqbal Z, McVean G (Bioinformatics) (Ad
  3 KB (297 words) - 22:22, 8 September 2020
• Minia
  GATB-Minia-Pipeline is a de novo assembly pipeline for Illumina data. It can assemble genomes and metagenomes. * Minia 3 (contigs assembly) based on the BCALM2 (unitigs assembly) tool
  2 KB (285 words) - 13:31, 15 August 2022

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