3.basecall-qc-correct-fetch.md

quality control of sequencing data

这个列表收集了短读长、长度长的质控工具。

数据模拟 | reads simulation

• [wgsim] - [C, Na, Na] - [Reads simulator.]
• [badread] - [Python, v0.4.1, 2024.2] - [a long read simulator that can imitate many types of read problems.]

basecall

• [Dorado] - [C++, v0.8.3, 2024.11] - [v0.9.0, 2024.12, with new dorado polish command] - [Oxford Nanopore's Basecaller.]

qc

• [FastQC] - [Java, 0.12.1, 2023.03] - [A quality control tool for high throughput sequence data.]
• [fastp] - [C++/C, v0.23.4, 2023.05] - [2018.09, Bioinformatics] - [fastp: an ultra-fast all-in-one FASTQ preprocessor.]
• [fastp] - [C++/C, v0.23.4, 2023.05] - [2023.05, iMeta] -[Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp.]
• [Trimmomatic] - [Java, v0.39, 2021.01] - [2014,04, Bioinformatics] - [Trimmomatic: a flexible trimmer for Illumina sequence data.]
• [Cutadapt] - [Python, v4.9, 2024.06] - [2010.na, EMBnet J] - [Cutadapt Removes Adapter Sequences From High-Throughput Sequencing Reads.]
• [FastUniq] - [C++, 1.1, 2012.05] - [2012.12, Plos ONE] - [FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads.]
• [[PoreChop][https://github.com/rrwick/Porechop]] - [C++, v0.2.4, 2018.10] - [adapter trimmer for Oxford Nanopore reads. Unsupported since Oct 2018]
• [Sickle] - [C, v1.33, 2014.7] - [Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files]
• [PEAT] - [C++, v1.2.4, 2016.2, No longer maintained, recommond EARRINGS] - [2015.1, BMC Bioinformatics] - PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm.]
• [EARRINGS] - [C++, v1.1.0, 2024.6] - [2021.7, Bioinformatics] - [EARRINGS: an efficient and accurate adapter trimmer entails no a priori adapter sequences]
• [NanoPack] - [Python, No release, ] - [2018.3, Bioinformatics] - [NanoPack: visualizing and processing long-read sequencing data.]
• [NanoPlot] - [Python, v1.42.0, 2023.10] - [2023.5, Bioinformatics] - [NanoPack2: population-scale evaluation of long-read sequencing data]
• [chopper] - [Rust, v0.9.0, 2024.8] - [2023.5, Bioinformatics] - [NanoPack2: population-scale evaluation of long-read sequencing data.]
• [nanoQC] - [Python, no release, na] - [2018.3, Bioinformatics] - [NanoPack: visualizing and processing long-read sequencing data]
• [fastplong] - [C++, v0.2.2, 2024.12] - [Ultra-fast preprocessing and quality control for long-read sequencing data]

correct

consensus sequences from long-reads

• [medaka] - [Python, v2.0.0, 2024.9] - [a tool to create consensus sequences and variant calls from nanopore sequencing data.]

fetch sequence from public databases

• SRA Toolkit - [C/C++, v3.1.1, 2024.5] - [The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.]
• KingFisher - [Python, v0.4.1, 2024.1] - [Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.]
• iSeq - [Shell, v1.2.0, 2024.10] - [2024.10, Bioinformatics] - [iSeq: An integrated tool to fetch public sequencing data.]