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146 public repositories
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An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
Versatile open-source tool for microbiome analysis
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Updated
May 14, 2020
Python
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
Viral genomics analysis pipelines
Updated
May 20, 2020
Python
An efficient FASTQ manipulation suite
Detect and visualize target mutations by scanning FastQ files directly
Simple FASTQ quality assessment using Python
Updated
May 29, 2018
Python
A collection of scripts and notes related to genomics and bioinformatics
FastQC port to Qt5: A quality control tool for high throughput sequence data.
💾 📃 "Reads to report" for public health and clinical microbiology
A DNA Sequence Alignment/Map (SAM) library for Clojure
Updated
Aug 18, 2020
Clojure
Efficient handling of FASTQ files from Python
Updated
May 2, 2020
Python
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
Updated
Jul 29, 2020
Python
Exome/Capture/RNASeq Pipeline Implementation using snakemake
Updated
Mar 26, 2018
Python
Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences
A golang package and a CLI for manipulating small k-mers (k <= 32) optional with Taxids but without frequency information
Randomly subsample sequencing reads to a specified coverage
Updated
Jun 26, 2020
Rust
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
Ultra-fast Multi-threaded FASTQ Demultiplexing
Parse and process FASTA and FASTQ formatted files of biological sequences.
Updated
Aug 16, 2020
Julia
Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI).
Updated
Oct 10, 2019
Java
Simulate metagenomic short reads from one or more populations.
Updated
Jun 7, 2020
Python
Updated
Mar 21, 2020
Rust
Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.
Sync paired-end FASTA/Q files and keep singleton reads
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Stefan Kurtz reported the following issue over our seqan-dev list:
I followed the description for the Cmake-setup and noticed in the example CMakeList.txt shown at the end of https://docs.seqan.de/seqan/3-master-user/setup.html that compiler optimization options such as -O3 is missing, which will lead to poor performance for users who do not recognize it.
I now use