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  • |{{#vardefine:app|snp-pipeline}} |{{#vardefine:url|https://github.com/CFSAN-Biostatistics/snp-pipeline}}
    3 KB (304 words) - 21:24, 6 December 2019
  • 3 KB (312 words) - 21:24, 6 December 2019
  • 4 KB (502 words) - 21:24, 6 December 2019

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  • ...line also supports detailed error reporting and easy resuming of runs. The pipeline has been tested on human, mouse and yeast ATAC-seq data and human and mouse ...ATAC-seq pipeline protocol definition is here. Some parts of the ATAC-seq pipeline were developed in collaboration with Jason Buenrostro, Alicia Schep and Wil
    3 KB (440 words) - 21:13, 6 December 2019
  • |{{#vardefine:app|snp-pipeline}} |{{#vardefine:url|https://github.com/CFSAN-Biostatistics/snp-pipeline}}
    3 KB (304 words) - 21:24, 6 December 2019
  • ...GERT utilizes several established bioinformatic tools combined into single pipeline which hides different technical quirks from an inexperienced user. ....com/articles/10.1186/s13100-019-0163-6 Guliaev AS, Semyenova SK. MGERT: a pipeline to retrieve coding sequences of mobile genetic elements from genome assembl
    3 KB (305 words) - 14:20, 15 September 2020
  • [[Category:Pipeline]] Lazypipe is a stand-alone pipeline for identifying viruses in host-associated or environmental samples. The ma
    4 KB (486 words) - 12:59, 1 June 2021
  • ...line, SNPhylo, to construct phylogenetic tree based on SNP data. With this pipeline, user can construct a phylogenetic tree from a file containing huge SNP dat Lee, T. H., Guo, H., Wang, X., Kim, C., & Paterson, A. H. (2014). SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. BMC Genomics, 15(1).
    3 KB (338 words) - 21:24, 6 December 2019
  • This package contains the pipeline for conducting a CUT&RUN analysis. The pipeline comprises of read trimming, alignment steps, motif finding steps, and final
    2 KB (266 words) - 22:20, 26 August 2020
  • ...ogy Meta Annotator for Plants (GOMAP) pipeline. GOMAP is a high-throughput pipeline to annotate GO terms to plant protein sequences.
    2 KB (263 words) - 22:13, 27 August 2020
  • The pipeline was originally developed for Illumina data, but thanks to the versatility o [https://academic.oup.com/nar/article/41/13/e129/1129833 MITObim pipeline described in Hahn et al. 2013]
    3 KB (301 words) - 15:20, 22 April 2020
  • zUMIs is a fast and flexible pipeline to process RNA-seq data with (or without) UMIs. The input to this pipeline is simply fastq files. In the most common cases, you will have a read conta
    2 KB (298 words) - 22:24, 26 August 2020
  • PhyloPhlAn is a computational pipeline for reconstructing highly accurate and resolved phylogenetic trees based on The pipeline is scalable to thousands of genomes and uses the most conserved 400 protein
    3 KB (293 words) - 21:23, 6 December 2019
  • ...bly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible assemblies, give it both Illumina reads and long rea
    2 KB (292 words) - 21:29, 6 December 2019
  • ...nd preparation. This is both a GUI and command line tool. The configurable pipeline includes image/diffusion information check, padding/Cropping of data, slice
    2 KB (290 words) - 21:50, 27 August 2020
  • ...nd preparation. This is both a GUI and command line tool. The configurable pipeline includes image/diffusion information check, padding/Cropping of data, slice
    2 KB (291 words) - 21:20, 6 December 2019
  • RepeatExplorer is a computational pipeline for discovery and characterization of repetitive sequences in eukaryotic genomes. The pipeline
    2 KB (278 words) - 21:24, 6 December 2019
  • MetaCompare is a computational pipeline for prioritizing resistome risk by estimating the potential for ARGs to be ...., Heath, L. S., Xia, K., & Zhang, L. (2018). MetaCompare: A computational pipeline for prioritizing environmental resistome risk. FEMS microbiology ecology.]
    3 KB (304 words) - 21:21, 6 December 2019
  • PIPITS is an automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences from the ...S. Read, Robert I. Griffiths and Karsten Schonrogge, PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illum
    3 KB (298 words) - 21:22, 6 December 2019
  • Redundans pipeline assists an assembly of heterozygous genomes. .../2457531 Leszek P. Pryszcz and Toni Gabaldón (2016) Redundans: an assembly pipeline for highly heterozygous genomes. NAR. doi: 10.1093/nar/gkw294]
    3 KB (332 words) - 21:24, 6 December 2019
  • MIDAS is an integrated pipeline that leverages >30,000 reference genomes to estimate bacterial species abun ...B Rodriguez-Mueller, N Garud, and KS Pollard. "An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biog
    3 KB (304 words) - 20:32, 7 January 2022
  •   HomBlocks is a new and highly efficient pipeline that used homologous blocks searching method to construct multi-gene alignm   In this pipeline, the core conserved fragment (conserved coding genes, functional non-coding
    4 KB (478 words) - 21:21, 6 December 2019
  • ...ense. The pipeline revised for 454 data was named CABOG (Miller 2008). The pipeline revised for PacBio/Oxford was named 'PBcR' (Berlin 2015).
    3 KB (361 words) - 21:29, 6 December 2019
  • Unified PHYling pipeline for phylogenomic data collection from annotated Stajich JE. 2017 PHYling: Phylogenomic pipeline from core markers on genomes to unassembled reads. https://github.com/staji
    3 KB (377 words) - 12:01, 1 July 2021
  • [[Category:Pipeline]] Mikado is a lightweight Python3 pipeline to identify the most useful or
    4 KB (495 words) - 21:50, 13 January 2022
  • Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes blast a ...cchia F, Basu S, Petrosino G, Salvemini M, Sanges R. Annocript: a flexible pipeline for the annotation of transcriptomes which can also identify putative long
    3 KB (387 words) - 21:18, 6 December 2019
  • ...erformance computing environment providing a scalability that makes this a Pipeline to Annotate Whole-genome Sequences (PAWS). The flexibility of evidences tha ...cles/10.1186/1746-4811-5-8 JC Estill and JL Bennetzen. 2009. "The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes." Pl
    3 KB (381 words) - 21:20, 6 December 2019
  • ...of each technology and assembly method if they were used in isolation. The pipeline is based on perl scripts and third-party open source software like the AMOS
    3 KB (390 words) - 21:20, 6 December 2019
  • ...igh-performance and automatic functional annotation tasks. This Annotation Pipeline allows your to integrate and automate your functional annotation task in a
    2 KB (275 words) - 19:42, 16 February 2018
  • -p PIPELINE_FILENAME, --pipeline=PIPELINE_FILENAME Load this pipeline file on startup
    7 KB (869 words) - 21:12, 6 December 2019
  • The pipeline is flexible, scalable and optimized. It can operate either on a single lapt ...t JP., Dekker J., Heard E., Barillot E. HiC-Pro: An optimized and flexible pipeline for Hi-C processing. Genome Biology 2015, 16:259 doi:10.1186/s13059-015-083
    3 KB (426 words) - 16:41, 28 June 2021
  • Stacks is a software pipeline for building loci out of a set of short-read sequenced samples. Stacks was The command line pipeline is available via the "stacks" environment module.
    4 KB (638 words) - 18:51, 9 June 2021
  • Fast-Plast is a pipeline that leverages existing and novel programs to quickly assemble, orient, and ...sembly implemented in afin to close gaps of contigs with low coverage. The pipeline then identifies regions from the quadripartite structure of the chloroplast
    4 KB (487 words) - 21:20, 6 December 2019
  • Description: Eukaryote Non-Model Transcriptome Annotation Pipeline
    2 KB (236 words) - 21:20, 6 December 2019
  • Description: a transcriptome assembly and mRNA annotation pipeline
    2 KB (236 words) - 21:21, 6 December 2019
  • A computational pipeline for processing Illumina sequence capture data
    2 KB (246 words) - 21:24, 6 December 2019
  • FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦
    2 KB (246 words) - 14:18, 10 July 2020
  • Bioinformatics pipeline for discovery of genetic variants from NGS reads.
    2 KB (237 words) - 21:24, 6 December 2019
  • A pipeline to identify miRNA binding sites from Ago2-CLIP data by de novo motif findin
    2 KB (252 words) - 21:21, 6 December 2019
  • This pipeline is designed to complete circular bacterial genomes using a sampling strateg
    2 KB (255 words) - 21:59, 26 August 2020
  • A versatile aligning pipeline for bisulfite sequencing data.
    2 KB (237 words) - 21:02, 6 December 2019
  • Mitofinder is a pipeline to assemble mitochondrial genomes and extract mitochondrial genes from trim
    2 KB (255 words) - 21:23, 6 December 2019
  • Phasing and SV Calling Pipeline
    2 KB (245 words) - 21:21, 6 December 2019
  • ...ter trimming, etc. They are primarily written to support an Illumina based pipeline - but should work with any FASTQs.
    2 KB (260 words) - 21:20, 6 December 2019
  • Quantas: A pipeline to analyze alternative splicing using RNA-Seq
    2 KB (249 words) - 21:24, 6 December 2019
  • |{{#vardefine:url|https://github.com/veg/flea-pipeline}} FLEA is a bioinformatics pipeline for analyzing longitudinal sequencing data from the Pacific Biosciences RS-
    2 KB (260 words) - 22:01, 27 August 2020
  • Toil is a scalable, efficient, cross-platform pipeline management system, written entirely in Python, and designed around the prin
    2 KB (260 words) - 21:29, 6 December 2019
  • BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneM
    2 KB (261 words) - 22:28, 26 August 2020
  • CWL-defined pipeline for using IDR to produce a set of peaks given two replicate eCLIP peaks
    2 KB (255 words) - 00:06, 3 March 2021
  • Denovo Genome Analysis Pipeline for Prokaryotic Species
    2 KB (272 words) - 21:20, 6 December 2019
  • Connectome Mapper 3 is an open-source Python3 image processing pipeline software that implements full anatomical, diffusion and resting-state MRI p
    2 KB (260 words) - 22:12, 26 August 2020
  • FineSTRUCTURE version 2, a pipeline for running ChromoPainter and FineSTRUCTURE for population inference. A GUI
    2 KB (246 words) - 21:21, 6 December 2019
  • Hyb is a bioinformatics pipeline for analysis of CLASH (crosslinking, ligation and sequencing of hybrids) da
    2 KB (247 words) - 21:22, 6 December 2019
  • rnaseqlib is a simple, lightweight pipeline for RNA-Seq analysis.
    2 KB (246 words) - 21:24, 6 December 2019
  • The Sashimi project develops the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics:
    2 KB (257 words) - 21:29, 6 December 2019
  • An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.
    2 KB (255 words) - 21:06, 6 December 2019
  • Connectome Mapper 3 implements a full diffusion MRI processing pipeline that understands BIDS datasets, from raw Diffusion / T1 / T2 data to multi-
    2 KB (269 words) - 15:13, 11 May 2020
  • This is a free pipeline released under the MIT license (See included file LICENSE for details). For
    2 KB (263 words) - 21:24, 6 December 2019
  • [[Category:Pipeline]]
    2 KB (279 words) - 20:59, 13 May 2021
  • fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses
    2 KB (280 words) - 22:04, 27 August 2020
  • metAMOS is an integrated assembly and analysis pipeline for metagenomic data. It is built around the Bambus2 metagenomic scaffolder
    2 KB (268 words) - 21:22, 6 December 2019
  • ...lyzing kilobase resolution Hi-C data. In this distribution, we include the pipeline for generating Hi-C maps from fastq raw data files and command line tools f
    2 KB (275 words) - 21:22, 6 December 2019
  • ...Reconstruction of Complex Structural Variants, or GROC-SVs, is a software pipeline for identifying large-scale structural variants, performing sequence assemb
    2 KB (274 words) - 21:21, 6 December 2019
  • ...and Parallelizable Association Container Toolbox) is a versatile software pipeline to perform various statistical tests for identifying genome-wide associatio
    2 KB (267 words) - 21:21, 6 December 2019
  • phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition o
    2 KB (279 words) - 00:09, 29 October 2020
  • ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identify
    2 KB (287 words) - 16:12, 24 November 2020
  • TAPIS (Transriptome Analysis Pipeline from Isoform Sequencing) is a program for correcting and aligning long read
    2 KB (272 words) - 21:29, 6 December 2019
  • This pangenome graph construction pipeline renders a collection of sequences into a pangenome graph (in the variation
    2 KB (287 words) - 19:56, 6 November 2020
  • ...a general-purpose Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline with a graphical and command-line interface. It offers a wide range of feat
    2 KB (290 words) - 22:04, 26 August 2020
  • construction pipeline. The blocks coordinates are output in GFF format and
    2 KB (284 words) - 18:44, 2 April 2021
  • RiboTaper is a new analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet p
    3 KB (293 words) - 13:48, 20 May 2020
  • An automated binning pipeline for single metagenomes, in particular host-associated and highly complex on
    3 KB (300 words) - 21:19, 6 December 2019
  • iRAP is a flexible RNA-seq analysis pipeline that allows the user to select and apply their preferred combination of exi
    3 KB (296 words) - 21:21, 6 December 2019
  • MetaLAFFA is a pipeline for annotating shotgun metagenomic data with abundances of functional ortho
    3 KB (305 words) - 13:52, 23 September 2021
  • ...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
  • ...genome assembly and mapping. We propose SeqyClean, a specialized cleaning pipeline that alleviates these issues.
    3 KB (303 words) - 21:24, 6 December 2019
  • PoPoolation is a pipeline for analysing pooled next generation sequencing data. Currently PoPoolation
    3 KB (321 words) - 21:23, 6 December 2019
  • ...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) - 12:15, 7 May 2021
  • 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
  • ...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 (299 words) - 21:21, 6 December 2019
  • ProtHint is a pipeline for predicting and scoring hints (in the form of
    3 KB (331 words) - 13:40, 30 April 2021
  • ...ecifying your inputs and analysis parameters. This input drives a parallel pipeline that handles distributed execution, idempotent processing restarts and safe
    3 KB (303 words) - 21:07, 6 December 2019
  • ...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_engine module to integrate any other third-party program in their pipeline.
    3 KB (311 words) - 15:22, 16 March 2020
  • 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
  • ...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 (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
  • Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seema
    3 KB (306 words) - 21:24, 6 December 2019
  • ...mbled nucleotide sequence. AMRFinderPlus is used in the Pathogen Detection pipeline, and these data are displayed in NCBI’s Isolate Browser. AMRFinderPlus re
    3 KB (330 words) - 18:42, 6 December 2021
  • Methylpy, a pyhton-based analysis pipeline for
    3 KB (309 words) - 21:21, 6 December 2019
  • ...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 (308 words) - 21:05, 6 December 2019
  • ...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 (326 words) - 21:24, 6 December 2019
  • ...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
  • PBJelly is a highly automated pipeline that aligns long sequencing reads
    3 KB (306 words) - 21:22, 6 December 2019
  • CCMetagen is a pipeline to classify organisms in metagenomes or metatranscriptomes accurately.
    3 KB (327 words) - 22:45, 3 January 2022
  • ...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 (318 words) - 21:24, 6 December 2019
  • HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance
    3 KB (329 words) - 21:21, 6 December 2019
  • ...tro, G. M., Cintra, L. C., Zerlotini, A., Lobo, F.P. POTION: an end-to-end pipeline for positive Darwinian selection detection in genomic scale data through ph
    3 KB (341 words) - 21:23, 6 December 2019
  • ...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
  • An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.
    3 KB (331 words) - 21:11, 6 December 2019
  • pVACseq A cancer immunotherapy pipeline for identifying and prioritizing neoantigens from a list of tumor mutations
    3 KB (334 words) - 21:23, 6 December 2019
  • ...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 (339 words) - 21:01, 6 December 2019
  • *PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Dolinsky TJ
    3 KB (338 words) - 21:22, 6 December 2019

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