Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Viral genomics analysis pipelines

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

Simple FASTQ quality assessment using Python

Efficient handling of FASTQ files from Python

My bioinfo toolbox

Frequently used commands in bioinformatics

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Versatile FASTA/FASTQ demultiplexer.

Benchmarking FASTQ compression with 'mature' compression algorithms

ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

Simulate metagenomic short reads from one or more populations.

mapping pipeline for ancient DNA

An ensemble method to recover corrupted FASTQ files, drop or fix pesky lines, remove unpaired reads, and settle reads interleaving.

MerCat: python code for versatile k-mer counting and diversity estimation for database independent property analysis for meta -ome data

This program dereplicates and/or filter nucleotide and/or protein database from a list of names or sequences (by exact match).

Pipeline for processing FASTQ data from an Illumina MiSeq to genotype human RNA viruses like HIV and hepatitis C

A collection of plots for long read sequencing FastQ files from devices like Oxford Nanopore's MinION and PromethION.

Sample an approximate number of reads from a fastq file without reading the entire file