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1. caltechdata_api – v1.10.1 - Added documentation and expanded cli options

   https://doi.org/10.22002/k51v8-cmz08  

   Morrell, Thomas E; Bhattarai, Rohan; Won, Elizabeth; Abakah, Alexander A; Nagi, Kshemaahna (July 2025, CaltechDATA)

   CLI Documentation for Users an expanded CLI file options CLI Documentation for Users by @Kshemaahna in https://github.com/caltechlibrary/caltechdata_api/pull/66 Expanded CLI file options by @Kshemaahna and @tmorrell New Contributors @Kshemaahna made their first contribution in https://github.com/caltechlibrary/caltechdata_api/pull/66 Full Changelog: https://github.com/caltechlibrary/caltechdata_api/compare/v1.10.0...v1.10.1 

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2. SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data

   https://doi.org/10.1093/bioinformatics/btac389  

   Ranjan, Piyush; Brown, Christopher A; Erb-Downward, John R; Dickson, Robert P (June 2022, Bioinformatics)

   Alkan, Can (Ed.)

   Abstract Summary Here, we introduce SNIKT, a command-line tool for sequence-independent visual confirmation and input-assisted removal of adapter contamination in whole-genome shotgun or metagenomic shotgun long-read sequencing DNA or RNA data. Availability and Implementation SNIKT is implemented in R and is compatible with Unix-like platforms. The source code, along with documentation, is freely available under an MIT license at https://github.com/piyuranjan/SNIKT. Supplementary information Supplementary data are available at Bioinformatics online. 

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3. CONSTAX2: improved taxonomic classification of environmental DNA markers

   https://doi.org/10.1093/bioinformatics/btab347  

   Liber, Julian A; Bonito, Gregory; Benucci, Gian Maria (May 2021, Bioinformatics)

   Marschall, Tobias (Ed.)

   Abstract Summary CONSTAX—the CONSensus TAXonomy classifier—was developed for accurate and reproducible taxonomic annotation of fungal rDNA amplicon sequences and is based upon a consensus approach of RDP, SINTAX and UTAX algorithms. CONSTAX2 extends these features to classify prokaryotes as well as eukaryotes and incorporates BLAST-based classifiers to reduce classification errors. Additionally, CONSTAX2 implements a conda-installable command-line tool with improved classification metrics, faster training, multithreading support, capacity to incorporate external taxonomic databases and new isolate matching and high-level taxonomy tools, replete with documentation and example tutorials. Availability and implementation CONSTAX2 is available at https://github.com/liberjul/CONSTAXv2, and is packaged for Linux and MacOS from Bioconda with use under the MIT License. A tutorial and documentation are available at https://constax.readthedocs.io/en/latest/. Data and scripts associated with the manuscript are available at https://github.com/liberjul/CONSTAXv2_ms_code. Supplementary information Supplementary data are available at Bioinformatics online. 

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4. dadi-cli: Automated and distributed population genetic model inference from allele frequency spectra

   https://doi.org/10.1101/2023.06.15.545182  

   Huang, Xin; Struck, Travis J; Davey, Sean W; Gutenkunst, Ryan N (June 2023, bioRxiv)

   Abstract Summarydadi is a popular software package for inferring models of demographic history and natural selection from population genomic data. But using dadi requires Python scripting and manual parallelization of optimization jobs. We developed dadi-cli to simplify dadi usage and also enable straighforward distributed computing. Availability and Implementationdadi-cli is implemented in Python and released under the Apache License 2.0. The source code is available athttps://github.com/xin-huang/dadi-cli. dadi-cli can be installed via PyPI and conda, and is also available through Cacao on Jetstream2https://cacao.jetstream-cloud.org/. 

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5. BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data

   https://doi.org/10.1093/genetics/iyac079  

   Steenwyk, Jacob L; Buida, Thomas J; Gonçalves, Carla; Goltz, Dayna C; Morales, Grace; Mead, Matthew E; LaBella, Abigail L; Chavez, Christina M; Schmitz, Jonathan E; Hadjifrangiskou, Maria; et al (May 2022, Genetics)

   Stajich, J (Ed.)

   Abstract Bioinformatic analysis—such as genome assembly quality assessment, alignment summary statistics, relative synonymous codon usage, file format conversion, and processing and analysis—is integrated into diverse disciplines in the biological sciences. Several command-line pieces of software have been developed to conduct some of these individual analyses, but unified toolkits that conduct all these analyses are lacking. To address this gap, we introduce BioKIT, a versatile command line toolkit that has, upon publication, 42 functions, several of which were community-sourced, that conduct routine and novel processing and analysis of genome assemblies, multiple sequence alignments, coding sequences, sequencing data, and more. To demonstrate the utility of BioKIT, we conducted a comprehensive examination of relative synonymous codon usage across 171 fungal genomes that use alternative genetic codes, showed that the novel metric of gene-wise relative synonymous codon usage can accurately estimate gene-wise codon optimization, evaluated the quality and characteristics of 901 eukaryotic genome assemblies, and calculated alignment summary statistics for 10 phylogenomic data matrices. BioKIT will be helpful in facilitating and streamlining sequence analysis workflows. BioKIT is freely available under the MIT license from GitHub (https://github.com/JLSteenwyk/BioKIT), PyPi (https://pypi.org/project/jlsteenwyk-biokit/), and the Anaconda Cloud (https://anaconda.org/jlsteenwyk/jlsteenwyk-biokit). Documentation, user tutorials, and instructions for requesting new features are available online (https://jlsteenwyk.com/BioKIT). 

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