Search results

• Galaxyml
  Galaxy-ML is a web machine learning end-to-end pipeline building framework, with special support to biomedical data.
  2 KB (284 words) - 14:51, 27 January 2023
• SeqyClean
  ...genome assembly and mapping. We propose SeqyClean, a specialized cleaning pipeline that alleviates these issues.
  3 KB (312 words) - 22:41, 21 August 2022
• IAssembler
  ...sing Sanger and/or Roche-454 pyrosequencing technologies into contigs. The pipeline gives much higher accuracy in EST assembly than other existing assemblers b
  3 KB (301 words) - 18:39, 15 August 2022
• MetaLAFFA
  MetaLAFFA is a pipeline for annotating shotgun metagenomic data with abundances of functional ortho
  3 KB (305 words) - 13:52, 23 September 2021
• V-pipe
  ...onski K., Metzner K.J., and Beerenwinkel N. 2021. "V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput sequencing data.
  3 KB (296 words) - 17:20, 22 August 2022
• Bamtofastq
  ...l should contain the same set of sequences that were input to the original pipeline run, although the order will not be preserved. The FASTQs will be emitted i
  3 KB (318 words) - 13:56, 8 March 2021
• Popoolation
  PoPoolation is a pipeline for analysing pooled next generation sequencing data. Currently PoPoolation
  3 KB (321 words) - 21:23, 6 December 2019
• Tbprofiler
  The tbprofiler pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then
  3 KB (312 words) - 21:31, 10 February 2023
• SQANTI
  SQANTI is a pipeline for the in-depth characterization of isoforms obtained by full-length trans
  3 KB (321 words) - 21:24, 6 December 2019
• ProtHint
  ProtHint is a pipeline for predicting and scoring hints (in the form of
  3 KB (329 words) - 20:27, 12 August 2022
• Roary
  Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seema
  3 KB (308 words) - 17:13, 10 June 2022
• REPdenovo
  ...ies, and can generate much longer repeats than existing tools. The overall pipeline is shown in the mannual file. REPdenovo supports the following main functio
  3 KB (327 words) - 21:43, 21 August 2022
• LongStitch
  A genome assembly correction and scaffolding pipeline using long reads, consisting of up to three steps:
  3 KB (314 words) - 19:00, 10 October 2022
• ContaVect
  ...s from gene therapy vector production after NGS sequencing. This automated pipeline can however be used for wider purpose requiring to identify map NGS dataset
  3 KB (309 words) - 20:40, 10 June 2022
• PBJelly
  PBJelly is a highly automated pipeline that aligns long sequencing reads
  3 KB (309 words) - 17:07, 21 August 2022
• REAPR
  ...eference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an asse
  3 KB (320 words) - 21:35, 21 August 2022
• Ampligraph
  An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.
  3 KB (315 words) - 14:44, 10 July 2023
• Necklace
  ...bly, in addition to using the reference annotation. Necklace is a software pipeline to run genome-guided and de novo assembly and combine the resulting transcr
  3 KB (312 words) - 21:22, 6 December 2019
• Pyrpipe
  ...pyrpipe_engine module to integrate any other third-party program in their pipeline.
  3 KB (311 words) - 15:22, 16 March 2020
• FEELnc
  This document is intended to give a technical description of the FEELnc pipeline in order to annotate long non-coding RNAs (lncRNAs) based on reconstructed
  3 KB (322 words) - 18:53, 10 July 2020
• Model Card Toolkit
  ...to a model's development and performance. Integrating the MCT into your ML pipeline enables the sharing model metadata and metrics with researchers, developers
  3 KB (333 words) - 15:31, 10 July 2023
• MarginPolish
  ...h serves as a standalone assembly polisher, it is also part of an assembly pipeline which includes an ultrafast nanopore assembler Shasta and a multi-task RNN
  3 KB (320 words) - 21:22, 6 December 2019
• FGMP
  FGMP (Fungal Genome Mapping Project) is a bioinformatic pipeline designed to provide in an unbiased manner an estimation of genome completen
  3 KB (326 words) - 21:20, 6 December 2019
• Methylpy
  Methylpy, a pyhton-based analysis pipeline for
  3 KB (309 words) - 21:21, 6 December 2019
• NpScarf
  ...draft genomes assemblies in real-time with Oxford Nanopore sequencing. The pipeline can run on a computing cluster as well as on a laptop computer for microbia
  3 KB (326 words) - 14:29, 4 September 2020
• CCMetagen
  CCMetagen is a pipeline to classify organisms in metagenomes or metatranscriptomes accurately.
  3 KB (327 words) - 22:45, 3 January 2022
• Crossmapper
  Crossmapper is an automated bioinformatics pipeline for asessing the rate of read crossmapping when two or more organisms are s
  3 KB (326 words) - 17:40, 31 January 2022
• Amphora2
  An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.
  3 KB (333 words) - 17:35, 10 June 2022
• AMOS
  ...so that new contributions can be easily inserted into an existing assembly pipeline. This modular design will foster the development of new assembly algorithms
  3 KB (344 words) - 12:41, 12 August 2022
• Talon
  A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification. Dana Wyman, Gabriela Balder
  3 KB (321 words) - 15:13, 23 September 2022
• ElPrep
  ...of the number of processing steps that need to be applied in a particular pipeline, greatly improving runtime performance.
  3 KB (345 words) - 21:20, 6 December 2019
• Pdb2pqr
  *PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Dolinsky TJ
  3 KB (336 words) - 17:51, 15 August 2022
• AutoDock-GPU
  included a batched ligand pipeline developed by Aaron Scheinberg from
  3 KB (332 words) - 15:25, 12 August 2022
• Seqmule
  ...ent, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file. SeqMule al
  3 KB (342 words) - 19:06, 15 September 2022
• Finder
  finder is a gene annotator pipeline which automates the process of
  3 KB (345 words) - 16:42, 15 August 2022
• WU BLAST
  ...st error checking identifies problems sooner; flexible identifiers improve pipeline design and management
  3 KB (356 words) - 17:44, 22 August 2022
• Hapdup
  HapDup (haplotype duplicator) is a pipeline to convert a haploid long read assembly into a dual diploid assembly. The r
  3 KB (324 words) - 21:07, 7 April 2022
• Haplomerger2
  HM2 is an easy-to-use automated pipeline for improving geneome assembly in the post-assembly stage. It consists of a
  3 KB (339 words) - 19:05, 12 August 2022
• Hapsembler
  The Hapsembler pipeline is described in contain three main stages:
  3 KB (332 words) - 18:15, 15 August 2022
• Meraculous
  ...mble human-sized genomes on commodity clusters in under a day. The process pipeline implements a highly transparent and portable model of job control and monit
  3 KB (354 words) - 18:36, 10 June 2022
• Rapidsai
  ...at integrates with a variety of machine learning algorithms for end-to-end pipeline accelerations without paying typical serialization costs. RAPIDS also inclu
  3 KB (348 words) - 21:29, 21 August 2022
• READemption
  READemption is a pipeline for the computational evaluation of RNA-Seq data. It was originally develop
  3 KB (352 words) - 17:58, 1 June 2022
• Nipype
  existing pipeline systems.
  3 KB (348 words) - 20:07, 12 August 2022
• Humann2
  HUMAnN 2.0 is a pipeline for efficiently and accurately profiling the presence/absence and abundance
  3 KB (348 words) - 22:26, 27 August 2020
• Aquamis
  AQUAMIS is a pipeline for routine assembly and quality assessment of microbial isolate sequencing
  3 KB (348 words) - 22:07, 20 October 2023
• PanX
  ...n-genome analysis, interactive visualization and exploration. The analysis pipeline is based on DIAMOND (Buchfink et al. 2015 Nature Methods), MCL and phylogen
  3 KB (346 words) - 21:22, 6 December 2019
• Biolite
  * A modular 'pipeline' framework with Python wrappers and workflows for commonly used NGS tools,
  3 KB (362 words) - 12:54, 15 August 2022
• RDnaTools
  ...ily the Mothur suite of utilities. Currently rDnaTools implements a single pipeline for the export, filtering, and cluster of 16S sequences.
  3 KB (361 words) - 21:24, 6 December 2019
• Mantis
  ...m needs a tumor BAM and a matched normal BAM file (produced using the same pipeline) to determine the instability score between the two samples within the pair
  3 KB (368 words) - 17:20, 27 May 2022
• Chewbbaca
  chewBBACA “BSR-Based Allele Calling Algorithm” is a comprehensive pipeline including a set of functions for the creation and validation of whole genom
  3 KB (346 words) - 15:58, 20 October 2023
• VirusDetect
  ...z D, Fuentes S, Ling K-S, Kreuze J, Fei Z (2017) VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs.]
  3 KB (377 words) - 23:22, 30 July 2020
• BiG-SCAPE
  ...ategory:Phylogenetics]][[Category:Biology]][[Category:Genomics]][[Category:Pipeline]]
  3 KB (377 words) - 12:53, 15 August 2022
• Blast2GO
  The Blast2GO Pipeline Version (B2G4Pipe) runs Blast2GO without graphical interface. The pipeline accepts BLAST and InterProScan results and parses
  6 KB (920 words) - 14:08, 16 March 2023
• Haphpipe
  HAplotype and PHylodynamics pipeline for viral assembly, population genetics, and phylodynamics.
  3 KB (405 words) - 16:40, 14 March 2023
• SNAP
  SNAP is a program that is part of a gene sequencing pipeline. It takes data from gene sequencing hardware that consists of short chunks
  3 KB (372 words) - 20:42, 12 August 2022
• SRAssembler
  SRAssembler (Selective Recursive local Assembler) is a modular pipeline program that can assemble genomic DNA reads into contigs that are homologou
  3 KB (381 words) - 15:33, 27 May 2022
• Deepvariant
  DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generati
  3 KB (356 words) - 13:17, 16 April 2024
• Wgs
  ...rge in 2004 as the wgs-assembler under the GNU General Public License. The pipeline revised for 454 data was named CABOG (Miller 2008).
  3 KB (375 words) - 20:55, 12 August 2022
• PerM
  ...ormat and that output can be further processed by ComB, SAMtools, RseqFlow pipeline and the [[Galaxy]]. Check the [http://code.google.com/p/perm/wiki/Manual ma
  3 KB (396 words) - 17:40, 21 August 2022
• Themisto
  ...Epidemiology with Mixed Samples. Supplement: Pseudoalignment in the mGEMS pipeline.
  3 KB (401 words) - 20:57, 3 June 2022
• MetaWRAP
  ...efull in your research, please cite the publication: MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis. If certain software wrapped
  3 KB (412 words) - 22:31, 8 September 2020
• Circos
  ...corporated into data acquisition, analysis and reporting pipelines (a data pipeline is a multi-step process in which data is analyzed by multiple and typically
  3 KB (409 words) - 13:35, 15 August 2022
• Maker
  MAKER is a portable and easily configurable genome annotation pipeline. It's purpose is to allow smaller eukaryotic and prokaryotic genome project
  3 KB (387 words) - 18:20, 18 August 2022
• GRIDSS
  ...t is hoped that GRIDSS can serve as an exemplar modular structural variant pipeline designed for interoperability with other tools.
  3 KB (388 words) - 21:20, 6 December 2019
• ARC
  ARC is a pipeline which facilitates iterative, reference guided ''de novo'' assemblies with t
  3 KB (430 words) - 14:32, 12 August 2022
• YAGO
  This is the pipeline to run YAGO 4. It allows to build YAGO 4 from a Wikidata dump.
  4 KB (480 words) - 17:13, 15 December 2022
• Amrfinderplus
  ...mbled nucleotide sequence. AMRFinderPlus is used in the Pathogen Detection pipeline, and these data are displayed in NCBI’s Isolate Browser. AMRFinderPlus re
  4 KB (447 words) - 15:59, 27 May 2022
• EDTA
  ...le Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline. Genome Biol. 20(1): 275.]
  4 KB (474 words) - 21:27, 14 September 2023
• Sickle
  ...ion is close. Illumina quality refers to qualities encoded with the CASAVA pipeline between versions 1.3 and 1.7. Illumina quality using CASAVA >= 1.8 is Sange
  4 KB (551 words) - 22:56, 21 August 2022
• Trimmomatic
  ...(using phred + 33 or phred + 64 quality scores, depending on the Illumina pipeline used), either uncompressed or gzipp'ed FASTQ. Use of gzip format is determi
  4 KB (522 words) - 20:52, 12 August 2022
• Galaxy
  ...ed collaborative environment, Galaxy's work history sharing and analytical pipeline building, as well as publishing and sharing the results in a convenient and
  4 KB (562 words) - 18:05, 9 November 2022
• Appreci8
  Appreci8 is a variant calling pipeline for detecting single nucleotide variants (SNVs) and short indels (up to 30
  4 KB (561 words) - 14:25, 12 August 2022
• GATK
  ...plementary tools to those available in those two packages. Our SNP calling pipeline (Q score recalibration -> multiple sequence realignment -> snp/index callin
  4 KB (540 words) - 16:53, 15 August 2022
• Biology
  ...turn, will provide the hardware and software support for the data analysis pipeline they create for you.
  4 KB (665 words) - 21:23, 14 December 2022
• Parabricks
  ...line and somatic analysis. The core of the Parabricks software is its data pipeline which takes raw data and transforms it according to the user's requirements
  4 KB (574 words) - 21:25, 14 December 2022
• Rnalysis
  If you use the Limma-Voom differential expression pipeline in your research, please cite:
  5 KB (648 words) - 16:12, 25 April 2023
• AlphaFold
  This package provides an implementation of the inference pipeline of AlphaFold v2.3. This is a completely new model that was entered in CASP1
  6 KB (832 words) - 15:38, 2 February 2024
• OrthoMCL
  ...-- that creates a suitable orthomcl.config file and automates much of the pipeline is provided:
  5 KB (748 words) - 22:40, 28 January 2024

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