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make alignment free its own module and updated TOC, footer, etc.
fix tables for real this time
Revert "fix the navigation tables on wiki pages" This reverts commit 1c78d5acac208efcaf4c284160febd715b2ddcb0.
fix the navigation tables on wiki pages
Updated de novo Transcript Assembly (markdown)
update ref-guided and de-novo mode to stringtie
update de novo assembly to use vars.
Update DE modes and Alternative Expression to use HISAT2 BAMs and simplified paths.
add flowchart
Remove redundant header syntax
Initial revision for Module2, Module3 and Module4