| Filename |
Size |
| Snakefile | 23.4K |
| summary.R | 17.1K |
| pipeline.sh | 12.1K |
| alignment_stats_extraction.sh | 6.6K |
| Step_10_preprocess_bam_for_metadmg.sh | 4.5K |
| taxa_stats_extraction.sh | 4.2K |
| Step_12_summary_and_plots.sh | 3.8K |
| Step_11_dna_damage_analysis.sh | 3.8K |
| plotEditDist.R | 3.8K |
| Step_5_extract_most_represented_assembly.sh | 3.3K |
| plotDamage.R | 3.3K |
| Step_4_reads_extraction_sample_subset.sh | 3.0K |
| reads_extraction_one_sample_all_target_genera.sh | 2.8K |
| Step_11_mapDamage.sh | 2.7K |
| Step_6_assemblies_to_index.sh | 2.6K |
| Step_4_reads_extraction.sh | 2.5K |
| Step_1_run_kraken_custum_patho_db.sh | 2.4K |
| Step_8_reads_index_file_generation.sh | 2.4K |
| Step_9_alignments.sh | 1.8K |
| Step_2_extact_genera.sh | 1.6K |
| sample_filtering.sh | 1.6K |
| run_kraken_test.sh | 1.5K |
| Step_3_translate_classification.sh | 1.4K |
| download_kraken_for_db.sh | 1.2K |
| Step_7_index_assemblies.sh | 1.2K |
| download_viral_for_db.sh | 1.1K |
| kraken_create_db.sh | 996 |
| create_viral_kraken_db.sh | 984 |
| generate_merged_fastq.sh | 980 |
| config.yml | 322 |