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sanger-pathogens/sh16_scripts

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legacy
legacy
 
 
modulefiles/sh16_scripts
modulefiles/sh16_scripts
 
 
modules
modules
 
 
pip
pip
 
 
Bayes_factor_comparison.py
Bayes_factor_comparison.py
 
 
Contig_stats.py
Contig_stats.py
 
 
Contig_summary.py
Contig_summary.py
 
 
Count_homopolymer_lengths.py
Count_homopolymer_lengths.py
 
 
Extract_CDS_from_alignment.py
Extract_CDS_from_alignment.py
 
 
Get_homoplasy_stats.py
Get_homoplasy_stats.py
 
 
README.md
README.md
 
 
bam_filter.py
bam_filter.py
 
 
bam_summary.py
bam_summary.py
 
 
bam_to_coverage_plot.py
bam_to_coverage_plot.py
 
 
bcf_2_pseudosequence.py
bcf_2_pseudosequence.py
 
 
change_fasta_taxon_names.py
change_fasta_taxon_names.py
 
 
change_tree_taxon_names.py
change_tree_taxon_names.py
 
 
fasta2fastq_shredder.py
fasta2fastq_shredder.py
 
 
filter_bcf.py
filter_bcf.py
 
 
fix_circular_bams.py
fix_circular_bams.py
 
 
iCANDY.py
iCANDY.py
 
 
join_dna_files_with_indels.py
join_dna_files_with_indels.py
 
 
multiple_mappings_to_bam.py
multiple_mappings_to_bam.py
 
 
pairwise_difference_count.py
pairwise_difference_count.py
 
 
pairwise_distances_from_tree.py
pairwise_distances_from_tree.py
 
 
prepare_BEAST_alignment.py
prepare_BEAST_alignment.py
 
 
reconstruct_snps_on_tree.py
reconstruct_snps_on_tree.py
 
 
remove_taxa_from_aln.py
remove_taxa_from_aln.py
 
 
remove_taxa_from_tree.py
remove_taxa_from_tree.py
 
 
replace_BEAST_blocks.py
replace_BEAST_blocks.py
 
 
root_tree.py
root_tree.py
 
 
run_RAxML.py
run_RAxML.py
 
 
summarise_snps.py
summarise_snps.py
 
 

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sh16_scripts

This repository contains a collection of scripts written by Simon Harris, former member of team 81. All scripts in the "legacy" subfolder are unmodified and represent the state deployed on farm3. The scripts extracted from that subfolder have been modified in order to run on farm5.

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Deprecated scripts for reference only

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