Merge branch 'atlassian_nuke' into 'master'

...ons/bioinformatics_tools/de_novo_assembly_tools/_index.md

...ations/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

...ns/bioinformatics_tools/downloading_sra_data_from_ncbi.md

...tions/bioinformatics_tools/pre_processing_tools/_index.md

...ons/bioinformatics_tools/pre_processing_tools/cutadapt.md

...ions/bioinformatics_tools/pre_processing_tools/prinseq.md

...tions/bioinformatics_tools/pre_processing_tools/scythe.md

...tions/bioinformatics_tools/pre_processing_tools/sickle.md

...s/bioinformatics_tools/pre_processing_tools/tagcleaner.md

...nformatics_tools/reference_based_assembly_tools/_index.md

...rmatics_tools/reference_based_assembly_tools/cufflinks.md

...cs_tools/removing_detecting_redundant_sequences/_index.md

...tics_tools/removing_detecting_redundant_sequences/cap3.md