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card_rgi: Anti-microbial gene screening for assemblies
filter_poly: Runs PrinSeq on paired-end FastQ files to remove low complexity sequences
kraken: Taxonomical identification of FastQ files
megahit: Metagenomic assembler for paired-end FastQ files
metaprob: Preforms read binning on metagenomic FastQ files
metamlst: Checks the Sequence Type of metagenomic FastQ reads using Multilocus Sequence Typing
metaspades: Metagenomic assembler for paired-end FastQ files
midas_species: Taxonomical identification of FastQ files on the species level
remove host: Read mapping with Bowtie2 against the host genome (default hg19) and removes the mapping reads
sistr: Salmonella in silico typing component for assemblies.
Features
Added inspect run mode to flowcraft for displaying the progress overview
during a nextflow run. This run mode has an overview and broadcast options
for viewing the progress of a pipeline.
Minor/Other changes
Changed mapping_patlas docker container tag and variable
(PR #76).
The env scope of nextflow.config now extends the PYTHONPATH
environmental variable.
Updated indexes for both mapping_patlas and mash based processes.
New logo!
Bug Fixes
Template: fastqc_report.py: Added fix to trim range evaluation.