moved things under Applications

...es/bioinformatics_tools/data_manipulation_tools/_index.md

...ormatics_tools/data_manipulation_tools/bamtools/_index.md

..._manipulation_tools/bamtools/running_bamtools_commands.md

...ormatics_tools/data_manipulation_tools/samtools/_index.md

..._manipulation_tools/samtools/running_samtools_commands.md

...ioinformatics_tools/data_manipulation_tools/sratoolkit.md

...des/bioinformatics_tools/de_novo_assembly_tools/_index.md

...ides/bioinformatics_tools/de_novo_assembly_tools/oases.md

...Guides/bioinformatics_tools/de_novo_assembly_tools/ray.md

...ioinformatics_tools/de_novo_assembly_tools/soapdenovo2.md

...nformatics_tools/de_novo_assembly_tools/trinity/_index.md

...sembly_tools/trinity/running_trinity_in_multiple_steps.md

...informatics_tools/de_novo_assembly_tools/velvet/_index.md

...embly_tools/velvet/running_velvet_with_paired_end_data.md

...vet/running_velvet_with_single_end_and_paired_end_data.md

...embly_tools/velvet/running_velvet_with_single_end_data.md

...es/bioinformatics_tools/downloading_sra_data_from_ncbi.md

...uides/bioinformatics_tools/pre_processing_tools/_index.md

...des/bioinformatics_tools/pre_processing_tools/cutadapt.md

...ides/bioinformatics_tools/pre_processing_tools/prinseq.md