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• 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

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