Commit 4f0b55ce authored by Susana MARTINEZ's avatar Susana MARTINEZ
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refinining readme file

parent f5956222
The **MgePrediction** module aims the identification/prediction of bacteriophage (VirSorter and VirFinder) and plasmid(cBar and PlasFLow) sequences from assembled contigs.
The **MgePrediction** module aims the identification/prediction of bacteriophage (VirSorter and VirFinder) and plasmid (cBar and PlasFLow) sequences from assembled contigs.
* **Inputs**: from IMP results; MGMT co-assembled contigs, MT contigs
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......@@ -4,9 +4,9 @@ The CRISPR-MGE pipeline identifies the CRISPRs from reads and contigs, and invas
## The pipeline contains the following workflows:
* [CRISPR prediction](CRISPR-prediction.md)
* [iMGEs prediction]**MgePrediction**: identification of bacteriophage (VirSorter and VirFinder) and plasmid(cBar and PlasFLow) sequences from assembled contigs
* **MgeDereplication**: collection of predicted MGEs and redundancy removal.
* **MgeRemapping**: remapping of all the reads aings the MGE contigs.
* [iMGEs prediction](CRISPR-prediction.md)
* [iMGEs dereplication](MGE-dereplication.md): collection of predicted MGEs and redundancy removal.
* [iMGEs remapping](MGE-remapping.md): remapping of all the metagenomic and metatranscriptomic reads to the iMGE sequences.
* **MgeHostLink**: identification of candidate hosts, their spacers composition and the link with the protospacer-containing contigs.
## Dependencies
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