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  • Short Sequence Assembly software.
    5 members (0 subcategories, 0 files) - 20:57, 12 August 2022
  • ...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
  • [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:Assembly]] ...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 (344 words) - 12:41, 12 August 2022
  • ...easy-to-use automated pipeline for improving geneome assembly in the post-assembly stage. It consists of a set of executables as well as wrappers for several ...elic relations between haplotype sequences in a highly-polymorphic diploid assembly, and then reconstruct and output two separated haploid sub-assemblies, the
    3 KB (339 words) - 19:05, 12 August 2022
  • ...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 (320 words) - 17:24, 10 June 2022
  • 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
  • ...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 (356 words) - 20:43, 11 August 2022
  • ...ntigs from an assembly, and help decide when to stop trying to improve the assembly.
    3 KB (316 words) - 17:17, 10 June 2022
  • A genome assembly correction and scaffolding pipeline using long reads, consisting of up to t * Tigmint cuts the draft assembly at potentially misassembled regions
    3 KB (314 words) - 21:33, 8 August 2022
  • |{{#vardefine:app|pb-assembly}} |{{#vardefine:url|https://github.com/PacificBiosciences/pb-assembly}}
    2 KB (265 words) - 21:22, 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) - 18:56, 12 August 2022
  • 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
  • ...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 (417 words) - 19:14, 10 June 2022
  • ...are two examples of how Purge Haplotigs can improve a haploid and diploid assembly.
    3 KB (356 words) - 20:27, 12 August 2022
  • ..., give it both Illumina reads and long reads, and it will conduct a hybrid assembly.
    2 KB (292 words) - 21:29, 6 December 2019
  • 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) - 17:50, 6 June 2022
  • ...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 (301 words) - 19:05, 12 August 2022
  • ...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) - 04:21, 19 February 2022
  • ...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 (340 words) - 20:47, 12 August 2022
  • [[Category:Software]][[Category:Biology]][[Category:Pipeline]][[Category:Assembly]] Automatic Assembly For The Fungi
    2 KB (245 words) - 20:45, 11 August 2022
  • ...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
  • ...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 (260 words) - 15:39, 10 June 2022
  • ..., 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
  • ...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
  • ...3Mb to 100Mb. The main feature of Zorro is the treatment before and after assembly to avoid errors.
    2 KB (280 words) - 16:17, 10 June 2022
  • ...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
  • ...ast sequence, Fast-Plast identifies chloroplast genes present in the final assembly.
    2 KB (288 words) - 20:23, 23 May 2022
  • 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) - 17:54, 6 June 2022
  • |{{#vardefine:app|assembly-stats}} |{{#vardefine:url|https://github.com/sanger-pathogens/assembly-stats}}
    2 KB (293 words) - 14:56, 12 August 2022
  • 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
  • ...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
  • ...and a set of semi-similar reference targets is available to initialize the assembly process.
    3 KB (430 words) - 14:32, 12 August 2022
  • 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
  • ...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
  • ...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
  • 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 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) - 19:20, 12 August 2022
  • 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
  • ...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 (312 words) - 20:43, 12 August 2022
  • ...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
  • 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
  • ...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 (378 words) - 17:52, 10 June 2022
  • * Assembly converter - map (liftover) data's coordinates to the current assembly.
    3 KB (333 words) - 18:52, 12 August 2022
  • Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types #genome assembly
    3 KB (332 words) - 19:05, 12 August 2022
  • ...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

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