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https://github.com/harrisonlab/popgen
12 April 2020, 03:54:10 UTC
History
Tip revision: 4f01d188df0fb1c73edd158bd81c7f404d82e273 authored by adarmitage on 10 October 2019, 16:56:08 UTC
Increased numbers of bootstrap reps.
Tip revision: 4f01d18
File Mode Size
README.md -rwxr-xr-x 4.2 KB
Translate6Frame.jar -rwxr-xr-x 98.5 KB
add_strand_column.py -rwxr-xr-x 428 bytes
add_strand_column2.py -rwxr-xr-x 470 bytes
additional_domains.sh -rwxr-xr-x 1.0 KB
ambiguous_to_unambiguous_fasta.py -rwxr-xr-x 1.1 KB
apple_renseq_part1.sh -rwxr-xr-x 3.3 KB
apple_renseq_part2.sh -rwxr-xr-x 4.9 KB
apple_renseq_part3.sh -rwxr-xr-x 1.7 KB
apple_renseq_part4.sh -rwxr-xr-x 2.9 KB
apple_renseq_part5.sh -rw-r--r-- 5.9 KB
apple_renseq_part6.sh -rw-r--r-- 830 bytes
bait_design.sh -rwxr-xr-x 1.8 KB
blast_matches_summary2.py -rw-r--r-- 3.3 KB
combine_1d_1d2_pass.py -rw-r--r-- 1.4 KB
create_baits.py -rwxr-xr-x 1.3 KB
download_reads.sh -rwxr-xr-x 4.4 KB
eliminate_wrong_repeat_entries.py -rwxr-xr-x 863 bytes
extract_rlk.py -rwxr-xr-x 615 bytes
fc_run.cfg -rwxr-xr-x 3.8 KB
filter_by_two_columns.py -rw-r--r-- 592 bytes
final_comparisons.sh -rwxr-xr-x 5.0 KB
find_matching_reads.py -rwxr-xr-x 1.4 KB
find_matching_reads2.py -rwxr-xr-x 1.1 KB
find_rpf3.sh -rw-r--r-- 7.3 KB
generate_trees_rlp_rlk_srlk.sh -rwxr-xr-x 1.0 KB
identification_of_atypical_genes.sh -rwxr-xr-x 7.2 KB
keep_list_genes2.py -rwxr-xr-x 1.0 KB
keep_out_genes.py -rwxr-xr-x 868 bytes
merge_overlaps_funcs.py -rwxr-xr-x 5.3 KB
merge_overlaps_funcs.pyc -rwxr-xr-x 5.4 KB
nanopore_emxfe_renseq.sh -rw-r--r-- 13.8 KB
nanopore_emxfe_renseq2.sh -rw-r--r-- 11.8 KB
nanopore_rgxha_renseq.sh -rw-r--r-- 2.3 KB
nlr_parser.sh -rwxr-xr-x 950 bytes
pacbio_emxfe.sh -rw-r--r-- 8.7 KB
plant_rgenes.sh -rwxr-xr-x 3.5 KB
remove_N_fasta.py -rwxr-xr-x 563 bytes
renseq_pre_snp_calling_prep.sh -rw-r--r-- 1.7 KB
rgaugury.sh -rwxr-xr-x 3.2 KB
stats_cds.R -rw-r--r-- 3.6 KB
stats_cds_emfe.R -rw-r--r-- 3.6 KB
stats_utr.R -rw-r--r-- 2.9 KB
stats_utr_emfe.R -rw-r--r-- 2.9 KB
strawberry_baits_blast_Hapil_ccs_3_99.ipynb -rw-r--r-- 4.3 MB
strawberry_reference_blast_Hapil_ccs_3_99.ipynb -rw-r--r-- 27.0 KB
strawberry_renseq_analysis_part1.sh -rw-r--r-- 3.3 KB
strawberry_renseq_part1.sh -rwxr-xr-x 2.0 KB
strawberry_renseq_part2.sh -rwxr-xr-x 4.9 KB
strawberry_renseq_part3.sh -rwxr-xr-x 4.5 KB
strawberry_renseq_reads_part1.sh -rwxr-xr-x 6.0 KB
strawberry_renseq_reads_part2.sh -rwxr-xr-x 6.9 KB
strawberry_renseq_reads_part3.sh -rwxr-xr-x 5.0 KB
strawberry_renseq_reads_part4.sh -rw-r--r-- 2.6 KB
strawberry_renseq_reads_part5.sh -rw-r--r-- 2.3 KB
sub_SMARTdenovo.sh -rw-r--r-- 1.2 KB
sub_blastn_renseq.sh -rw-r--r-- 537 bytes
sub_bwa_mem.sh -rwxr-xr-x 1.0 KB
sub_bwa_nanopolish.sh -rw-r--r-- 1.1 KB
sub_canu_correct.sh -rw-r--r-- 1.6 KB
sub_canu_renseq.sh -rwxr-xr-x 838 bytes
sub_canu_renseq2.sh -rwxr-xr-x 1.2 KB
sub_cluster_baits.sh -rwxr-xr-x 712 bytes
sub_fast_masking.sh -rwxr-xr-x 579 bytes
sub_fasta_subsample.sh -rwxr-xr-x 545 bytes
sub_fastq_sort.sh -rwxr-xr-x 262 bytes
sub_fasttree.sh -rwxr-xr-x 365 bytes
sub_gatk_canu_emily.sh -rw-r--r-- 1.4 KB
sub_gatk_canu_emily2.sh -rw-r--r-- 1.4 KB
sub_gatk_canu_fenella.sh -rw-r--r-- 1.4 KB
sub_gatk_canu_fenella2.sh -rw-r--r-- 1.4 KB
sub_gatk_lorma_emily.sh -rw-r--r-- 1.4 KB
sub_gatk_lorma_emily2.sh -rw-r--r-- 1.4 KB
sub_gatk_lorma_fenella.sh -rw-r--r-- 1.4 KB
sub_gatk_lorma_fenella2.sh -rw-r--r-- 1.4 KB
sub_get_sorted_paired_reads.sh -rwxr-xr-x 1.0 KB
sub_hmmscan.sh -rwxr-xr-x 622 bytes
sub_interproscan.sh -rwxr-xr-x 397 bytes
sub_lorma.sh -rw-r--r-- 500 bytes
sub_mafft.sh -rwxr-xr-x 469 bytes
sub_nanocorrect.sh -rw-r--r-- 779 bytes
sub_nanopolish_extract.sh -rw-r--r-- 491 bytes
sub_nanopolish_variants.sh -rw-r--r-- 1.9 KB
sub_ngsutils_sort.sh -rwxr-xr-x 399 bytes
sub_nlrparser.sh -rwxr-xr-x 850 bytes
sub_pairfq.sh -rwxr-xr-x 845 bytes
sub_phobius.sh -rwxr-xr-x 421 bytes
sub_pilon_3_libs.sh -rwxr-xr-x 2.1 KB
sub_plant_rgenes.sh -rwxr-xr-x 471 bytes
sub_poretools_demultiplex.sh -rw-r--r-- 1.3 KB
sub_poretools_trim.sh -rw-r--r-- 1.2 KB
sub_racon.sh -rw-r--r-- 1.6 KB
sub_read_qc.sh -rwxr-xr-x 1.5 KB
sub_read_qc_single.sh -rw-r--r-- 1.3 KB
sub_read_qc_single_pacbio.sh -rw-r--r-- 1.3 KB
sub_repeat_masker.sh -rwxr-xr-x 1.9 KB
sub_rgaugury.sh -rwxr-xr-x 1021 bytes
sub_seqkit.sh -rwxr-xr-x 253 bytes
sub_tophat_alignment.sh -rwxr-xr-x 2.0 KB
sub_trinity_assembly.sh -rwxr-xr-x 1.0 KB
test.py~ -rwxr-xr-x 0 bytes
the_really_really_final_bait_design_part1.sh -rwxr-xr-x 5.2 KB
the_really_really_final_bait_design_part2.sh -rwxr-xr-x 2.4 KB
the_really_really_final_bait_design_part3.sh -rwxr-xr-x 5.6 KB
transcriptome_prep.sh -rwxr-xr-x 3.5 KB
trim-h5.py -rwxr-xr-x 1.0 KB
ultimate_bait_design.sh -rwxr-xr-x 10.0 KB
welsh_onion.sh -rwxr-xr-x 4.5 KB
write_seq_length.py -rwxr-xr-x 482 bytes

README.md

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