Search results

• Ragout
  ...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) - 21:29, 21 August 2022
• Fast-Plast
  ...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
• TGICL
  ...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
• AAFTF
  [[Category:Software]][[Category:Biology]][[Category:Pipeline]][[Category:Assembly]] Automatic Assembly For The Fungi
  2 KB (245 words) - 20:45, 11 August 2022
• Hapdup
  ...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
• Hapsembler
  [[Category:Software]][[Category:Biology]][[Category:Assembly]] Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types
  3 KB (332 words) - 18:15, 15 August 2022
• LIGR
  [[Category:Software]][[Category:Biology]][[Category:Assembly]] LIGR Assembler is a sequence assembly program. It was derived from TIGR Assembler and addresses some of TIGR Asse
  2 KB (249 words) - 19:55, 15 August 2022
• Evigene
  ...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
• Trans-ABySS
  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
• ATRAM
  ..., 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
• Xander
  ...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
• Zorro
  ...3Mb to 100Mb. The main feature of Zorro is the treatment before and after assembly to avoid errors.
  2 KB (284 words) - 17:54, 22 August 2022
• FALCON unzip
  ...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
• FastPlast
  ...ast sequence, Fast-Plast identifies chloroplast genes present in the final assembly.
  2 KB (288 words) - 20:23, 23 May 2022
• Triobinning
  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) - 13:31, 15 August 2022
• Newbler
  [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Assembly]][[Category:De Novo]] Newbler is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the
  2 KB (305 words) - 16:17, 19 August 2022
• Assembly-stats
  |{{#vardefine:app|assembly-stats}} |{{#vardefine:url|https://github.com/sanger-pathogens/assembly-stats}}
  2 KB (293 words) - 14:56, 12 August 2022
• Clover
  [[Category:Assembly]] k-mers.Clover achieves a superior assembly quality in terms of corrected
  2 KB (296 words) - 13:47, 15 August 2022
• DEXTRACTOR
  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
• HAPCUT
  [[Category:Software]][[Category:Biology]][[Category:Assembly]] HapCUT is a max-cut based algorithm for haplotype assembly that uses the mix of sequenced fragments from the two chromosomes of an ind
  2 KB (298 words) - 18:13, 15 August 2022
• 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

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