refinining readme file

MGE-prediction.md

-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
 

README.md

@@ -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