Search results

• 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
• 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
• HapCUT2
  accuracy. We found that previously described haplotype assembly methods are Edge, P., Bafna, V. & Bansal, V. HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Genome Res. gr.213462.116 (2016). doi:
  3 KB (317 words) - 20:03, 8 March 2022
• Inspector
  Inspector is a tool for assembly evaluation with long read data. The input includes a contig file, long read ...-02527-4 Chen, Y., Zhang, Y., Wang, A.Y. et al. Accurate long-read de novo assembly evaluation with Inspector. Genome Biol 22, 312 (2021).]
  3 KB (319 words) - 18:50, 15 August 2022
• Consed
  calling, sequence comparisons, and sequence assembly. Phred, Cross_match, ...encing reactions to perform, and facilitating checking the accuracy of the assembly using digest and forward/reverse pair information.
  3 KB (348 words) - 18:39, 12 August 2022
• SOAPdenovo
  ...enovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble
  2 KB (314 words) - 00:05, 22 August 2022
• MECAT
  MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alig ...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
• 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
• Ensembl Tools
  * Assembly converter - map (liftover) data's coordinates to the current assembly.
  3 KB (333 words) - 18:52, 12 August 2022
• Meraculous
  ...ansparent and portable model of job control and monitoring where different assembly stages can be executed and re-executed separately or in unison on a wide va
  3 KB (354 words) - 18:36, 10 June 2022
• Racon
  ...as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step, such as Miniasm. ...which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while provi
  3 KB (364 words) - 21:24, 21 August 2022

View (previous 20 | next 20) (20 | 50 | 100 | 250 | 500)