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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
  • Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences.
    3 KB (367 words) - 21:21, 6 December 2019
  • ...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
  • ...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 (352 words) - 21:22, 6 December 2019
  • 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 (329 words) - 21:21, 6 December 2019
  • ...order and orient the intermediate contigs/scaffolds assembled in a genome assembly project, in a process known as Scaffolding. OPERA is based on an exact algo
    3 KB (362 words) - 21:23, 6 December 2019
  • ...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 (365 words) - 21:24, 6 December 2019
  • ...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: 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 (387 words) - 21:20, 6 December 2019
  • ...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) - 15:06, 4 March 2021
  • ...ome organisms where a reference genome is available or where a manual post-assembly process of improvement is being undertaken at the Wellcome Trust Sanger Ins
    3 KB (390 words) - 21:20, 6 December 2019
  • ...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 (359 words) - 21:21, 6 December 2019
  • * A2Amapper: ATAC, Assembly to Assembly Comparision tool:
    3 KB (384 words) - 21:21, 6 December 2019
  • ...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
  • 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 (474 words) - 19:33, 15 April 2021
  • ...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 (479 words) - 14:32, 9 October 2020
  • ...ced with 'N' symbols. Occasionally, if the genome is in the early stage of assembly the non-masked sequences are too short for most reference indexes to be bui
    2 KB (361 words) - 20:47, 5 April 2018
  • 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.
    4 KB (565 words) - 17:34, 30 June 2021
  • Automatic Assembly For The Fungi
    2 KB (239 words) - 21:00, 7 June 2021
  • Description: a transcriptome assembly and mRNA annotation pipeline
    2 KB (236 words) - 21:21, 6 December 2019
  • RACA: Reference-Assisted Chromosome Assembly
    2 KB (233 words) - 21:24, 6 December 2019
  • ipyrad, an interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, d
    2 KB (243 words) - 21:21, 6 December 2019
  • Assemblytics: a web analytics tool for the detection of variants from an assembly
    2 KB (252 words) - 17:02, 29 September 2020
  • NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.
    2 KB (250 words) - 13:32, 23 June 2020
  • Purge haplotigs and overlaps in an assembly based on read depth
    2 KB (257 words) - 15:07, 20 April 2020
  • clustering and de novo assembly.
    2 KB (254 words) - 21:24, 6 December 2019
  • ...ombines multiple whole genome de novo assemblies into a combined consensus assembly using the best segments of the individual assemblies.
    2 KB (248 words) - 21:21, 6 December 2019
  • ...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
  • Reago an assembly tool for 16S ribosomal RNA recovery from metagenomic data
    2 KB (274 words) - 21:24, 6 December 2019
  • A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX
    2 KB (252 words) - 21:24, 6 December 2019
  • Genome assembly scaffolding using information from paired-end/mate-pair libraries, long rea
    2 KB (271 words) - 21:24, 6 December 2019
  • ...libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.
    2 KB (265 words) - 14:30, 4 September 2020
  • Clview is an nteractive tool for inspecting the ACE format assembly files generated by CAP3 or phrap.
    2 KB (254 words) - 21:05, 6 December 2019
  • LIGR Assembler is a sequence assembly program. It was derived from TIGR Assembler and addresses some of TIGR Asse
    2 KB (247 words) - 21:21, 6 December 2019
  • Fast reference-guided genome assembly scaffolding
    2 KB (263 words) - 15:27, 13 August 2020
  • Multi-sample de novo assembly and variant calling using Linked de bruijn graphs. Variant calling with and
    2 KB (271 words) - 21:21, 6 December 2019
  • REAGO an assembly tool for 16S ribosomal RNA recovery from metagenomic data
    2 KB (250 words) - 21:24, 6 December 2019
  • ...r high-resolution genealogical relationship of bacterial isolates with WGS assembly data.
    2 KB (283 words) - 21:20, 6 December 2019
  • Short read RNASeq de novo assembly is a well established method to study transcription of organisms lacking a
    2 KB (280 words) - 21:20, 6 December 2019
  • # The length cutoff used for seed reads usef for pre-assembly
    2 KB (248 words) - 20:31, 2 August 2021
  • ...ww.genomebiology.com/2012/13/12/R122 Ray Meta: scalable de novo metagenome assembly and profiling. Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis
    2 KB (269 words) - 21:24, 6 December 2019
  • ...36-3 Zhang, S. V, Zhuo, L., & Hahn, M. W. (2016). AGOUTI: improving genome assembly and annotation using transcriptome data. GigaScience, 5(1), 1.12. doi:10.11
    2 KB (265 words) - 21:02, 6 December 2019
  • ...eline for identifying large-scale structural variants, performing sequence assembly at the breakpoints, and reconstructing the complex structural variants usin
    2 KB (274 words) - 21:21, 6 December 2019
  • ...tegory:Biology]][[Category:Bioinformatics]][[Category:Genomics]][[Category:Assembly]]
    2 KB (283 words) - 21:21, 6 December 2019
  • ...KB Seah, Elmar Pruesse. phyloFlash — Rapid SSU rRNA profiling and targeted assembly from metagenomes.]
    2 KB (279 words) - 00:09, 29 October 2020
  • A tool to order and orient genome assembly contigs via Minimap2 alignments to a reference genome.
    2 KB (280 words) - 21:24, 6 December 2019
  • ...Li. 2018. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. bioRxiv, 256479.]
    2 KB (275 words) - 21:21, 6 December 2019
  • # The length cutoff used for seed reads usef for pre-assembly
    2 KB (266 words) - 20:30, 2 August 2021
  • Newbler is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the
    2 KB (290 words) - 21:22, 6 December 2019
  • ...ge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples)
    2 KB (293 words) - 14:54, 23 February 2021
  • aTRAM does targeted ''de novo'' assembly of loci from paired-end Illumina runs and consists of the following tools:
    2 KB (274 words) - 21:12, 6 December 2019

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