fastk

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  "desc": "K-mer counter for high-fidelity shotgun datasets",
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  "full_name": "fastk",
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  "github_readme_excerpt": "# FastK: A K-mer counter (for HQ assembly data sets)\n  \n\u003cfont size =\"4\"\u003e**_Author:  Gene Myers_**\u003cbr\u003e\n**_First:   July 22, 2020_**\u003cbr\u003e\n**_Current: April 18, 2021_**\u003c/font\u003e\n\n- [Command Line](#command-line)\n  - [FastK](#fastk)\n  - [Fastrm, Fastcp, \u0026 Fastmv](#fastrm)\n  - [Fastmerge](#fastmerge)\n  - [Fastcat](#fastcat)\n\n- [HPC Operation](#hpc)\n\n- [Core Applications](#core-applications)\n  - [Histex](#histex): Display a FastK histogram or convert to 1-code\n  - [Tabex](#tabex): List, Check, find a k\u0026#8209;mer in a FastK table, or convert to 1-code\n  - [Profex](#profex): Display a FastK profile or convert to 1-code\n  - [Logex](#logex): Combine kmer,count tables with logical expressions \u0026 filter with count cutoffs\n  - [Symmex](#symmex): Produce a symmetric k-mer table from a canonical one\n  - [KmerMap](#kmermap): Produce a .bed file showing all the regions in a target covered by a set of k-mers\n\n- [C-Library Interface](#c-library-interface)\n  - [K-mer Histogram Class](#k-mer-histogram-class)\n  - [K-mer Table Class](#k-mer-table-class)\n  - [K-mer Stream Class](#k-mer-stream-class)\n  - [K-mer Profile Class](#k-mer-profile-class)\n \n- [File Encodings](#file-encodings)\n  - [`.hist`: K-mer Histogram File](#k-mer-histogram-file)\n  - [`.ktab`: K-mer Table Files](#k-mer-table-files)\n  - [`.prof`: K-mer Profile Files](#k-mer-profile-files)\n\n\n\u003ca name=\"command-line\"\u003e\u003c/a\u003e\n\n## Command Line\n\nFastK is a k\u0026#8209;mer counter that is optimized for processing high quality DNA assembly data\nsets such as those produced with an Illumina instrument or a PacBio run in HiFi mode.\nFor example it is about 2 times faster than KMC3 when counting 40-mers in a 50X HiFi data\nset.  Its relative speedup decreases with increasing error rate or increasing values of k,\nbut regardless is a general program that works for any DNA sequence data set and choice of k.\nIt is further designed to handle data sets of arbitrarily large size, e.g. a 100X data\nset of a 32GB Axolotl genome (3.2Tbp) can be performed on a machin",
  "github_repo": "thegenemyers/FASTK",
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  "license": "BSD-3-Clause AND (MIT AND BSD-3-Clause) AND MIT",
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  "name": "fastk",
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