About debug messages in knitr
When writing markdown documents for processing with knitr, warnings and messages are usually shown in the output document. Often, I also want to print debug messages to the console, e.g. for indicating progress etc.
Paper: Snakemake workflows for long-read bacterial genome assembly and evaluation
2024-04-01 | #Assembly #ONT #Paper #Snakemake
My paper on two Snakemake workflows for bacterial genome assembly now published in GigaByte: Snakemake workflows for long-read bacterial genome assembly and evaluation. The first workflow, called ont-assembly-snake, is used for generating multiple genome assemblies from long-read sequencing data of a bacterial isolate.
Paper: Nosocomial outbreak of Pandoraea commovens
2023-11-15 | #Clinical Diagnostics #Paper
Our paper about a nosocomial outbreak of Pandoraea spp. was recently published in Emerging Infections Diseases: Outbreak of Pandoraea commovens Infections among Non-Cystic Fibrosis Intensive Care Patients, Germany, 2019-2021 In total, 24 patients from 4 hospitals in Berlin were affected.
One Snakemake workflow for paired-end and single-end data, with globbing
2023-11-09 | #Snakemake
After figuring out how to make one Snakefile that can deal with both single-end and paired-end sequencing files in one workflow, I was still missing a puzzle piece: How to deal with globbing to get the fastq files in the rule’s input section.
One Snakemake workflow for paired-end and single-end data
2023-10-24 | #Snakemake
Recently, I was thinking about how to set up a Snakemake workflow that can deal with both single-end and paired-end sequencing datasets. For Illumina, paired-end sequencing results in two FASTQ files for each sample: one file with the forward reads and one file with the reverse reads, which have R1 and R2 in the file names.