rework Merge attempt

...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

...ic/bioinformatics_tools/downloading_sra_data_from_ncbi.md

...cific/bioinformatics_tools/pre_processing_tools/_index.md

...fic/bioinformatics_tools/pre_processing_tools/cutadapt.md

...ific/bioinformatics_tools/pre_processing_tools/prinseq.md

...cific/bioinformatics_tools/pre_processing_tools/scythe.md

...cific/bioinformatics_tools/pre_processing_tools/sickle.md

...c/bioinformatics_tools/pre_processing_tools/tagcleaner.md

...t/applications/app_specific/bioinformatics_tools/qiime.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

...cs_tools/removing_detecting_redundant_sequences/cd_hit.md

content/applications/app_specific/dmtcp_checkpointing.md

content/applications/app_specific/fortran_c_on_hcc.md

content/applications/app_specific/mpi_jobs_on_hcc.md

content/applications/app_specific/running_gaussian_at_hcc.md