gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
gapFinisher to process SSPACE-LongRead output to fill gaps after the scaffolding. gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6733440/1464 days ago
sunbeam: A robust, extensible metagenomics pipeline
Sunbeam is a pipeline written in snakemake that simplifies and automates many of the steps in metagenomic sequencing analysis. It uses conda to manag...1429 days ago
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SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis
.... A presentation about SHAMAN is available here and a poster here. More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03666-41370 days ago
URMAP, an ultra-fast read mapper
...map and may therefore pose an unrealistically easy challenge to read mappers and variant callers. More at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7320720/...1296 days ago
Understanding pango networks !
...ment-of-nomenclature-rules/ https://www.pango.network/how-does-the-system-work/what-are-pango-lineages/ Reference paper https://www.nature.com/articles/s41564-020-0770-5944 days ago
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Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
..., we introduce assembly quality and completeness metrics that account for the expected genomic copy numbers. More at https://www.nature.com/articles/s41592-022-01445-y...775 days ago
GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
...f the GenomeQC pipeline is available in the GitHub repository https://github.com/HuffordLab/GenomeQC. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6568-2730 days ago