Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens
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May 12, 2025 - Python
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amplicon-sequencing
Here are 10 public repositories matching this topic...
A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment
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May 12, 2025 - Python
gNOMO2 allows integrated multi-omics analyses of microbiomes
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Aug 7, 2024 - Python
Python package for microsatellite genotyping from highly multiplexed amplicon sequencing data
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Feb 6, 2024 - Python
A pipeline for variant calling from P. falciparum short reads generated from Illumina and ONT libraries
variant-calling malaria oxford-nanopore illumina-sequencing amplicon-sequencing plasmodium-falciparum
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Dec 20, 2023 - Python
CRISPRSeqSim is a tool that simulates results of CRISPR/cas editing fragments target sequencing.
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Jul 10, 2023 - Python
A snakemake pipeline for amplicon (16S, 18S, ITS) sequence analysis using Usearch.
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Jul 25, 2023 - Python
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Dec 19, 2022 - Python
Pipeline for amplicon sequencing projects. OTUs can be build with various methods (usearch,vsearch,uparse,swarm) and classified using the RDP Classifier and SINA. Final output is a BIOM file for downstream processing (Phyloseq/R)
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Dec 18, 2023 - Python
Bioinformatics pipeline for processing Hantavirus NGS data with a two-pass approach. Implements quality control, reference-based mapping, metaconsensus refinement, variant calling, and automatic negative sample detection. Features include primer evaluation, coverage visualization, and comparison between consensus sequences.
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May 29, 2025 - Python
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