Merge branch 'rework' into 'master'

...p_specific/bioinformatics_tools/alignment_tools/bowtie.md

..._specific/bioinformatics_tools/alignment_tools/bowtie2.md

...ecific/bioinformatics_tools/alignment_tools/bwa/_index.md

...rmatics_tools/alignment_tools/bwa/running_bwa_commands.md

...fic/bioinformatics_tools/alignment_tools/clustal_omega.md

...ic/bioinformatics_tools/alignment_tools/tophat_tophat2.md

...tions/app_specific/bioinformatics_tools/biodata_module.md

...ic/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

...fic/bioinformatics_tools/de_novo_assembly_tools/_index.md

...ific/bioinformatics_tools/de_novo_assembly_tools/oases.md

...ecific/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