Search results

• 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
• DRAP
  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
• Shovill
  ...uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assem
  2 KB (286 words) - 18:13, 23 August 2022
• FALCON fc run cfg
  # The length cutoff used for seed reads usef for pre-assembly
  2 KB (248 words) - 20:31, 2 August 2021
• PRICE
  ...es from such complex datasets, and it is also being applied to the de novo assembly of large individual genomes.
  2 KB (286 words) - 16:26, 10 June 2022
• GROCSVs
  ...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
• PhyloFlash
  ...KB Seah, Elmar Pruesse. phyloFlash — Rapid SSU rRNA profiling and targeted assembly from metagenomes.]
  2 KB (279 words) - 00:09, 29 October 2020
• BRIG
  ...arisons between a large number of genomes, with a focus on handling genome assembly data.
  2 KB (278 words) - 16:25, 10 June 2022
• RaGOO
  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
• GetOrganelle
  ...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
• FALCON fc large run cfg
  # The length cutoff used for seed reads usef for pre-assembly
  2 KB (266 words) - 20:30, 2 August 2021
• Read2tree
  ...allows a user to bypass several standard steps, including read filtering, assembly, gene prediction, gene annotation, all vs. all comparisons, orthology predi
  2 KB (292 words) - 18:42, 12 July 2023
• Haploflow
  ...ritz, A., Bremges, A., Deng, ZL. et al. Haploflow: strain-resolved de novo assembly of viral genomes. Genome Biol 22, 212 (2021)]
  2 KB (287 words) - 20:31, 3 January 2022
• SCOP
  [[Category:Assembly]]
  2 KB (295 words) - 17:31, 15 August 2022
• Crass
  [[Category:Software]][[Category:Biology]][[Category:Assembly]]
  3 KB (300 words) - 14:02, 15 August 2022
• Medaka
  ...works applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can b
  2 KB (290 words) - 14:37, 21 August 2023
• Kvarq
  ...s in FastQ format. Mapping to a whole-genome reference sequence or de novo assembly or the short reads is not necessary.
  2 KB (287 words) - 15:26, 21 June 2023
• Raven
  [[Category:Software]][[Category:assembly]]
  2 KB (284 words) - 21:14, 20 November 2023
• HapCompass
  HapCompass implements a novel HAPCOMPASS algorithm for haplotype assembly of densely sequenced human genome data. The algorithm operates on a graph w
  2 KB (287 words) - 18:13, 15 August 2022
• SMARTdenovo
  ...e novo assembler for PacBio and Oxford Nanopore (ONT) data. It produces an assembly from all-vs-all raw read alignments without an error correction stage. It a
  2 KB (296 words) - 21:24, 6 December 2019
• FLASh
  ...gnificantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.
  2 KB (297 words) - 16:44, 15 August 2022
• NOVOPlasty
  ...290925 Dierckxsens N., Mardulyn P. and Smits G. (2016) NOVOPlasty: De novo assembly of organelle genomes from whole genome data. Nucleic Acids Research, doi: 1
  3 KB (310 words) - 21:23, 6 December 2019
• StringMLST
  ...sequencing reads. stringMLST predicts the ST of an isolate in a completely assembly and alignment free manner. The tool is designed in a light-weight, platform
  2 KB (292 words) - 20:45, 12 August 2022
• Supernova
  |{{#vardefine:url|https://support.10xgenomics.com/de-novo-assembly/software/}} Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library
  3 KB (306 words) - 16:55, 10 June 2022
• Hifiasm
  ...ces a new graph binning algorithm and achieves the best haplotype-resolved assembly given trio data.
  3 KB (303 words) - 22:23, 27 August 2020
• YAK
  ...ific use cases: 1) to robustly estimate the base accuracy of CCS reads and assembly contigs, and 2) to investigate the systematic error rate of CCS reads. It a
  2 KB (293 words) - 16:10, 10 March 2021
• Mccortex
  Multi-sample de novo assembly and variant calling using Linked de bruijn graphs. Variant calling with and
  3 KB (297 words) - 22:22, 8 September 2020
• DASTool
  ...are generated independently when all binning tools are applied to the same assembly.
  3 KB (315 words) - 21:21, 6 December 2019
• YASRA
  YASRA (Yet Another Short Read Assembler) performs comparative assembly of short reads using a reference genome, which can differ substantially fro
  3 KB (304 words) - 20:56, 12 August 2022
• SeqyClean
  ...ise, which is presented as low-quality bases, has serious impact on genome assembly and mapping. We propose SeqyClean, a specialized cleaning pipeline that all
  3 KB (312 words) - 22:41, 21 August 2022
• Trycycler
  ...assemblies for the same isolate, Trycycler can combine them into a single assembly that is better than any of your inputs.
  3 KB (305 words) - 18:13, 22 July 2021

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