/Athaliana/20180508_geoduck_assemblies_bowtie2_indexes


Directory contains Bowtie2 reference genome index files for three P.generosa genome assemblies.

Index files were generated using the bowtie2-build command.


All commands were run in a Jupyter Notebook. See the notebook entry (linked below) for full info on reference assemblies used as inputs and link to Jupyter Notebook.



Files:

- *PGA*.bt2 : Bowtie2 index files for Phase Genomics Hi-C assembly.

- *PGA*.err : Bowtie2 stderr file for Phase Genomics Hi-C index creation.

- *PGA*.out : Bowtie2 stdout file for Phase Genomics Hi-C index creation.

- *duck4-p*.bt2 : Bowtie2 index files for Phase Genomics Hi-C assembly.

- *duck4-p*.err : Bowtie2 stderr file for Phase Genomics Hi-C index creation.

- *duck4-p*.out : Bowtie2 stdout file for Phase Genomics Hi-C index creation.

- *sparse*.bt2 : Bowtie2 index files for Phase Genomics Hi-C assembly.

- *sparse*.err : Bowtie2 stderr file for Phase Genomics Hi-C index creation.

- *sparse*.out : Bowtie2 stdout file for Phase Genomics Hi-C index creation.

Notebook entry:

http://onsnetwork.org/kubu4/2018/05/09/read-mapping-mapping-illumina-data-to-geoduck-genome-assemblies-with-bowtie2/