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BAM-merge_bams.sh
BAM-merge_bams.sh
 
 
FP022.finalSNPs.vcf.gz
FP022.finalSNPs.vcf.gz
 
 
FP085.finalSNPs.vcf.gz
FP085.finalSNPs.vcf.gz
 
 
FP096.finalSNPs.vcf.gz
FP096.finalSNPs.vcf.gz
 
 
README.txt
README.txt
 
 
VCF-print_segregating_sites.pl
VCF-print_segregating_sites.pl
 
 
VCFS-merge_chunks_to_vcf.sh
VCFS-merge_chunks_to_vcf.sh
 
 
VCFS-merge_squared_recalled_vcfs_by_chunk.sh
VCFS-merge_squared_recalled_vcfs_by_chunk.sh
 
 
VCFS-vcfs2raxml-cx2-capability_queue.sh
VCFS-vcfs2raxml-cx2-capability_queue.sh
 
 
VCFS-vcfs2raxml.sh
VCFS-vcfs2raxml.sh
 
 
VCFtoFASTA.sh
VCFtoFASTA.sh
 
 
add_wt_strains.py
add_wt_strains.py
 
 
alignPE_bwa.sh
alignPE_bwa.sh
 
 
alignPE_bwa_multiref.sh
alignPE_bwa_multiref.sh
 
 
align_bwa.sh
align_bwa.sh
 
 
assemble_canu.sh
assemble_canu.sh
 
 
assemble_sr_spades.sh
assemble_sr_spades.sh
 
 
assembly_spades_trustedcontigs.sh
assembly_spades_trustedcontigs.sh
 
 
bowtie_contaminents.sh
bowtie_contaminents.sh
 
 
deco_bbmap.sh
deco_bbmap.sh
 
 
deco_bowtie.sh
deco_bowtie.sh
 
 
even_doodies_can_count_SNPers.py
even_doodies_can_count_SNPers.py
 
 
fastq_wrapper.sh
fastq_wrapper.sh
 
 
freebayes_calling_01-individual_samples.sh
freebayes_calling_01-individual_samples.sh
 
 
freebayes_calling_02-merging_samples_to_positionlist.sh
freebayes_calling_02-merging_samples_to_positionlist.sh
 
 
freebayes_calling_03-recall_samples_at_known_positions_cx1_version.sh
freebayes_calling_03-recall_samples_at_known_positions_cx1_version.sh
 
 
gene_snp_script.py
gene_snp_script.py
 
 
genomic_variants.sh
genomic_variants.sh
 
 
hybridspades_force.sh
hybridspades_force.sh
 
 
indexbam_samtools.sh
indexbam_samtools.sh
 
 
isolates.py
isolates.py
 
 
jos_raxml_bootstrap.sh
jos_raxml_bootstrap.sh
 
 
kihansi_mapping.sh
kihansi_mapping.sh
 
 
kihansi_merge_vcf.sh
kihansi_merge_vcf.sh
 
 
mada_mapping.sh
mada_mapping.sh
 
 
mark_duplicates.sh
mark_duplicates.sh
 
 
medusa_scaffold.sh
medusa_scaffold.sh
 
 
medusa_scaffold_force.sh
medusa_scaffold_force.sh
 
 
mergebams_crosslane_picard.sh
mergebams_crosslane_picard.sh
 
 
mergebams_picard.sh
mergebams_picard.sh
 
 
mergevariants_gatk.sh
mergevariants_gatk.sh
 
 
mkdup_gatk.sh
mkdup_gatk.sh
 
 
multi_sample_variants_gatk.sh
multi_sample_variants_gatk.sh
 
 
nanoplot.sh
nanoplot.sh
 
 
ngmlr_mapping.sh
ngmlr_mapping.sh
 
 
nucdna_map_to_ref_split_lanes.sh
nucdna_map_to_ref_split_lanes.sh
 
 
pipeline.sh
pipeline.sh
 
 
pipeline_2.sh
pipeline_2.sh
 
 
pipeline_loop.sh
pipeline_loop.sh
 
 
plink_bed_create.sh
plink_bed_create.sh
 
 
polish_assembly_pilon.sh
polish_assembly_pilon.sh
 
 
polish_racon.sh
polish_racon.sh
 
 
rdgrps_picard.sh
rdgrps_picard.sh
 
 
realign_gatk.sh
realign_gatk.sh
 
 
recall_variants_gatk.sh
recall_variants_gatk.sh
 
 
run_maker.sh
run_maker.sh
 
 
run_raxml.sh
run_raxml.sh
 
 
selectSNP_gatk.sh
selectSNP_gatk.sh
 
 
sewell_raxml_bootstrap.sh
sewell_raxml_bootstrap.sh
 
 
split_bd_genome_to_chunks.R
split_bd_genome_to_chunks.R
 
 
trim.sh
trim.sh
 
 
trimPE_cutadapt.sh
trimPE_cutadapt.sh
 
 
trim_cutadapt.sh
trim_cutadapt.sh
 
 
tsv2fasta.R
tsv2fasta.R
 
 
variants_gatk.sh
variants_gatk.sh
 
 
variants_sniffles.sh
variants_sniffles.sh
 
 
vcf2fasta_gatk.sh
vcf2fasta_gatk.sh
 
 
vcf2phylip2raxml.sh
vcf2phylip2raxml.sh
 
 
zip_tabix.sh
zip_tabix.sh
 
 

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Specific to Imperial HPC qsub conditions

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