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
• SEQuel
  ...contain a substantial number of errors that need to be corrected after the assembly process. The algorithm behind SEQuel makes use of a graph structure called
  3 KB (382 words) - 22:39, 21 August 2022
• Maq
  Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences.
  3 KB (377 words) - 19:47, 12 August 2022
• Tigmint
  ...inked reads from 10x Genomics Chromium. The reads are first aligned to the assembly, and the extents of the large DNA molecules are inferred from the alignment ...rg Bohlmann, Steven J.M. Jones and Inanc Birol (2018). Tigmint: correcting assembly errors using linked reads from large molecules. BMC Bioinformatics, 19(1).]
  3 KB (370 words) - 21:29, 6 December 2019
• VirusDetect
  ...s to the known virus reference database (GenBank gbvrl) as well as de novo assembly using Velvet with automated parameter optimization. The assembled contigs a
  3 KB (377 words) - 23:22, 30 July 2020
• FALCON
  Falcon: a set of tools for fast aligning long reads for consensus and assembly ...kit is a set of simple code collection which I use for studying efficient assembly algorithm for haploid and diploid genomes. It has some back-end code implem
  3 KB (395 words) - 15:19, 15 August 2022
• SRAssembler
  ...mbler repository is the distribution point of our code for selective local assembly of genomic regions matching a homologous query protein or DNA sequence. ...Chou, and Volker P. Brendel (2018) SRAssembler: Selective Recursive local Assembly of homologous genomic regions.]
  3 KB (381 words) - 15:33, 27 May 2022
• MEGAHIT
  ...oil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG c ...HIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics, doi: 10.1093/bioinformatics/b
  3 KB (367 words) - 18:31, 18 August 2022
• GRIDSS
  ...based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence. ...specific genomic rearrangement detection using positional de Bruijn graph assembly. Genome Research, 2017 doi: 10.1101/gr.222109.117]
  3 KB (388 words) - 21:20, 6 December 2019
• Wengan
  identifies miss-assemblies at different steps of the assembly process. For more information ...., Buena-Atienza, E., Ossowski, S. and Sagot,M-F. Efficient hybrid de novo assembly of human genomes with WENGAN. Nature Biotechnology (2020),
  4 KB (472 words) - 20:55, 12 August 2022
• PsiCLASS
  ...robust with the aggregation method used, including the built-in voting and assembly-based approaches such as StringTie-merge and TACO. Therefore, it can be eff ...nd Florea, L. A multi-sample approach increases the accuracy of transcript assembly. Nat Commun 10, 5000 (2019)]
  4 KB (480 words) - 15:00, 14 December 2022
• TACO
  TACO: Multi-sample transcriptome assembly from RNA-Seq
  2 KB (234 words) - 18:53, 1 June 2022
• RACA
  RACA: Reference-Assisted Chromosome Assembly
  2 KB (235 words) - 19:45, 10 June 2022
• BUSCO
  BUSCO stands for Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Ortholo BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
  5 KB (607 words) - 19:38, 27 March 2023
• FRAMA
  Description: a transcriptome assembly and mRNA annotation pipeline
  2 KB (236 words) - 21:21, 6 December 2019
• Ipyrad
  ipyrad, an interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, d
  2 KB (239 words) - 19:00, 15 August 2022
• MetaBCC-LR
  ...bly helps to enhance the assembly quality while significantly reducing the assembly cost in terms of time and memory usage. The efficiency and accuracy of Meta
  6 KB (774 words) - 14:28, 15 December 2022
• Assemblytics
  Assemblytics: a web analytics tool for the detection of variants from an assembly
  2 KB (252 words) - 17:02, 29 September 2020
• Asset
  ...acbio, 10X, Bionano, HiC) to accumulate the support evidence for a de novo assembly.
  2 KB (253 words) - 20:07, 15 June 2023
• NECAT
  NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.
  2 KB (250 words) - 13:32, 23 June 2020
• Clview
  Clview is an nteractive tool for inspecting the ACE format assembly files generated by CAP3 or phrap.
  2 KB (252 words) - 13:48, 15 August 2022
• PurgeDups
  Purge haplotigs and overlaps in an assembly based on read depth
  2 KB (257 words) - 18:50, 27 May 2022
• Rainbow
  clustering and de novo assembly.
  2 KB (254 words) - 21:24, 6 December 2019
• Staden
  A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX
  2 KB (254 words) - 15:59, 22 August 2022
• Skmer
  ...mes from low-coverage sequencing reads (genome-skims), without needing any assembly or alignment step.
  2 KB (260 words) - 13:31, 15 August 2022
• WhatsHap
  ...ts using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short r
  2 KB (269 words) - 21:29, 6 December 2019
• JCVI
  ...libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.
  2 KB (265 words) - 14:30, 4 September 2020
• Yagcloser
  [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:Assembly]]
  2 KB (265 words) - 19:07, 1 April 2024
• RagTag
  Fast reference-guided genome assembly scaffolding
  2 KB (263 words) - 15:27, 13 August 2020
• Pbipa
  ...ved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi reads to produce h
  2 KB (268 words) - 21:58, 27 April 2022
• Fast-gep
  ...r high-resolution genealogical relationship of bacterial isolates with WGS assembly data.
  2 KB (283 words) - 15:46, 22 July 2022

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