Commit 989ac593 authored by Claire Hoede's avatar Claire Hoede
Browse files

Correct skip parameter for assembly filtering

parent cd1fafc8
Pipeline #61005 skipped with stage
......@@ -21,7 +21,7 @@ metagWGS is split into different steps that correspond to different parts of the
* assembles cleaned reads (combined with `S01_CLEAN_QC` step) or raw reads (combined with `--skip_clean` parameter) ([metaSPAdes](https://github.com/ablab/spades) or [Megahit](https://github.com/voutcn/megahit))
* assesses the quality of assembly ([metaQUAST](http://quast.sourceforge.net/metaquast))
* deduplicates cleaned reads (combined with `S01_CLEAN_QC` step) or raw reads (combined with `--skip_clean` parameter) ([BWA](http://bio-bwa.sourceforge.net/) + [Samtools](http://www.htslib.org/) + [Bedtools](https://bedtools.readthedocs.io/en/latest/))
* `S03_FILTERING` (can be stopped at with `--stop_at_filtering` ; can be skipped with `--skip_assembly`)
* `S03_FILTERING` (can be stopped at with `--stop_at_filtering` ; can be skipped with `--skip_filtering`)
* filters contigs with low CPM value ([Filter_contig_per_cpm.py](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/master/bin/Filter_contig_per_cpm.py) + [metaQUAST](http://quast.sourceforge.net/metaquast))
* `S04_STRUCTURAL_ANNOT` (can be stopped at with `--stop_at_structural_annot`)
* makes a structural annotation of genes ([Prokka](https://github.com/tseemann/prokka) + [Rename_contigs_and_genes.py](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/master/bin/Rename_contigs_and_genes.py))
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