aMeta: an accurate and memory-efficient ancient Metagenomic profiling workflow
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posted on 2023-07-04, 09:21 authored by Nikolay OskolkovNikolay Oskolkov, Claudio MirabelloClaudio Mirabello, Per UnnebergPer UnnebergaMeta is a Snakemake workflow for identifying microbial sequences in ancient DNA shotgun metagenomics samples. The workflow performs:
- trimming adapter sequences and removing reads shorter than 30 bp with Cutadapt
- quality control before and after trimming with FastQC and MultiQC
- taxonomic sequence kmer-based classification with KrakenUniq
- sequence alignment with Bowtie2 and screening for common microbial pathogens
- deamination pattern analysis with MapDamage2
- Lowest Common Ancestor (LCA) sequence alignment with Malt
- authentication and validation of identified microbial species with MaltExtract
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NBISContact email
nikolay.oskolkov@scilifelab.seSciLifeLab acknowledgement
- Bioinformatics platform (NBIS)
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