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  • Short Sequence Assembly software.
    3 members (0 subcategories, 0 files) - 20:43, 21 September 2012
  • ...BAM (ONT reads aligned to the assembly), and it produces a polished FASTA assembly. ...rginPolish serves as a standalone assembly polisher, it is also part of an assembly pipeline which includes an ultrafast nanopore assembler Shasta and a multi-
    3 KB (320 words) - 21:22, 6 December 2019
  • Redundans pipeline assists an assembly of heterozygous genomes. ...ddition, Redundans will automatically close the gaps resulting from genome assembly or scaffolding.
    3 KB (332 words) - 21:24, 6 December 2019
  • ...n. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls. ...://www.genomebiology.com/2013/14/5/R47/ REAPR: a universal tool for genome assembly evaluation. Genome Biology 2013, 14:R47, doi:10.1186/gb-2013-14-5-r47.]
    3 KB (318 words) - 21:24, 6 December 2019
  • ...and improve in hopes of eventually becoming a widely accepted and deployed assembly infrastructure. In this sense, AMOS is both a design philosophy and a softw
    3 KB (339 words) - 21:01, 6 December 2019
  • ...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 (352 words) - 21:11, 6 December 2019
  • ...ntigs from an assembly, and help decide when to stop trying to improve the assembly.
    3 KB (314 words) - 21:29, 6 December 2019
  • |{{#vardefine:app|pb-assembly}} |{{#vardefine:url|https://github.com/PacificBiosciences/pb-assembly}}
    2 KB (265 words) - 21:22, 6 December 2019
  • Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not inclu Racon is a great polishing tool that can be used to clean up assembly errors. It's also very fast and well suited for long-read data. However, it
    3 KB (338 words) - 14:53, 9 December 2019
  • Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are th ...128 virtual processors and 1952 GB of memory). The compute cost of such an assembly is around $20 at AWS spot market or reserved prices.
    3 KB (402 words) - 21:24, 6 December 2019
  • ..., give it both Illumina reads and long reads, and it will conduct a hybrid assembly.
    2 KB (292 words) - 21:29, 6 December 2019
  • DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation) consists of two component packages, R ...er design as an objective function. In addition, for each contig within an assembly, RSEM-EVAL provides a score that assesses how well that contig is supported
    4 KB (476 words) - 21:20, 6 December 2019
  • ...is a prototype genome assembly tool based on maximizing likelihood of the assembly in a model encompaasing error rate, insert length and other features of ind
    2 KB (279 words) - 21:20, 6 December 2019
  • Assembly Likelihood Estimator ALE is a probabalistic framework for determining the likelihood of an assembly given the data (raw reads) used to assemble it. It allows for the rapid dis
    2 KB (285 words) - 21:11, 6 December 2019
  • ...rst computes a set of candidate contig connections from the raw (original) assembly that are supported by the RNA-seq data. Then, in an optional step, the user ...rch/Rascaf/ Song, L., Shankar, D. and Florea, L. "Rascaf: Improving Genome Assembly with RNA-seq Data", The Plant Genome, 2016. doi: 10.3835/plantgenome2016.03
    3 KB (416 words) - 21:24, 6 December 2019
  • ...rmation is constructed with the compressed reads to enable the final-stage assembly. DBG2OLC: Efficient Assembly of Large Genomes Using the Compressed Overlap Graph. Chengxi Ye, Chris Hill
    3 KB (429 words) - 21:20, 6 December 2019
  • ...y in EST assembly than other existing assemblers by employing an iterative assembly strategy and automated error corrections of mis-assemblies. ...53 Zheng Y, Zhao L, Gao J, Fei Z. (2011) iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences. BMC Bioinformatics 12:453]
    3 KB (299 words) - 21:21, 6 December 2019
  • ...ulti-FASTA file (and an optional peer quality values file) and outputs the assembly files as produced by CAP3
    2 KB (320 words) - 21:29, 6 December 2019
  • ...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
  • ...ulti-FASTA file (and an optional peer quality values file) and outputs the assembly files as produced by CAP3
    3 KB (342 words) - 21:29, 6 December 2019
  • ...onditions for optimal assembly as well as algorithms for achieving optimal assembly.
    3 KB (334 words) - 21:24, 6 December 2019
  • ...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
  • 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 (258 words) - 21:29, 6 December 2019
  • ...und the Bambus2 metagenomic scaffolder and includes many current tools for assembly, gene finding, and taxonomic classification. For more details see the gitHu
    2 KB (268 words) - 21:22, 6 December 2019
  • ...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 (380 words) - 21:29, 6 December 2019
  • ...3Mb to 100Mb. The main feature of Zorro is the treatment before and after assembly to avoid errors.
    2 KB (278 words) - 21:29, 6 December 2019
  • ...genomes, if available, to assemble only target-alike reads. After initial assembly, it can also use existing genomes to perform guided merging of contigs. For ...Qu, Elizabeth M. Ryan, Michael C. Zody, and Matthew R. Henn (2012) De novo assembly of highly diverse viral populations. BMC Genomics 13:475.
    3 KB (371 words) - 21:29, 6 December 2019
  • |{{#vardefine:app|assembly-stats}} |{{#vardefine:url|https://github.com/sanger-pathogens/assembly-stats}}
    2 KB (291 words) - 21:11, 6 December 2019
  • ...icBiosciences/FALCON/wiki/FALCON-FALCON-Unzip-%22For-Phased-Diploid-Genome-Assembly-with-Single-Molecule-Real-Time-Sequencing%22
    3 KB (302 words) - 21:21, 6 December 2019
  • [[Category:Assembly]] k-mers.Clover achieves a superior assembly quality in terms of corrected
    2 KB (296 words) - 20:57, 12 May 2021
  • 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
  • ...and a set of semi-similar reference targets is available to initialize the assembly process.
    3 KB (425 words) - 21:01, 6 December 2019
  • 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 (440 words) - 21:20, 6 December 2019
  • ...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 (434 words) - 21:22, 6 December 2019
  • ...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 (294 words) - 21:24, 6 December 2019
  • KmerGenie estimates the best k-mer length for genome de novo assembly. Given a set of reads, KmerGenie first computes the k-mer abundance histogr ...org/content/30/1/31 Informed and Automated k-Mer Size Selection for Genome Assembly], HiTSeq 2013. [http://arxiv.org/pdf/1304.5665v1.pdf on arXiv]
    3 KB (323 words) - 21:21, 6 December 2019
  • ...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
  • ...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
  • ...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 (538 words) - 22:24, 27 August 2020
  • ...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
  • ...ry construction is completely revamped, resulting in major performance and assembly improvements. ..., 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
    3 KB (319 words) - 21:05, 6 December 2019
  • 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 (317 words) - 22:16, 19 January 2022
  • ...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 (302 words) - 21:24, 6 December 2019
  • ...t outputs may be plasmids, phages, etc. Recycler uses only features of the assembly graph (contig overlaps, lengths, and coverage level information) and alignm
    3 KB (316 words) - 21:24, 6 December 2019
  • 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) - 21:03, 6 December 2019
  • 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 (326 words) - 21:21, 6 December 2019
  • [[Category:Software]][[Category:biology]][[Category:NGS]][[Category:de novo assembly]] ..., Borodina T, Himmelbauer H SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Research 2007 17: 1697-170
    3 KB (314 words) - 21:24, 6 December 2019
  • ...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 (326 words) - 21:10, 6 December 2019
  • ...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 (376 words) - 21:24, 6 December 2019
  • * Assembly converter - map (liftover) data's coordinates to the current assembly.
    3 KB (333 words) - 21:20, 6 December 2019

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