Name		Name	Last commit message	Last commit date
Latest commit History 12 Commits
.gitignore		.gitignore
README.md		README.md
SNP_PCA.R		SNP_PCA.R
Vero-sharks_csv-filter.py		Vero-sharks_csv-filter.py
allele2numeric_matrix.py		allele2numeric_matrix.py
angsd.sh		angsd.sh
avg-cov-gencov-summary.py		avg-cov-gencov-summary.py
batch-012geno-vcftools.sh		batch-012geno-vcftools.sh
batch-blast-uniprot.sh		batch-blast-uniprot.sh
batch-blast-uniprot_nhr.sh		batch-blast-uniprot_nhr.sh
batch-blastp-uniprot.sh		batch-blastp-uniprot.sh
batch-bowtie2-build.sh		batch-bowtie2-build.sh
batch-bowtie2-fq-paired.sh		batch-bowtie2-fq-paired.sh
batch-bowtie2-fq-paired_whitesharks.sh		batch-bowtie2-fq-paired_whitesharks.sh
batch-bowtie2-local-genom_on_contigs-paired-cyp.sh		batch-bowtie2-local-genom_on_contigs-paired-cyp.sh
batch-bowtie2-softclipping-relaxed.sh		batch-bowtie2-softclipping-relaxed.sh
batch-bt2-softclip-rel-NO_dedup.sh		batch-bt2-softclip-rel-NO_dedup.sh
batch-bt2-whitesharks.sh		batch-bt2-whitesharks.sh
batch-bwa-index.sh		batch-bwa-index.sh
batch-bwa-mem-pe-cyp.sh		batch-bwa-mem-pe-cyp.sh
batch-clean_gms.sh		batch-clean_gms.sh
batch-extract_contigs.sh		batch-extract_contigs.sh
batch-fastqc.sh		batch-fastqc.sh
batch-filter-assembly.sh		batch-filter-assembly.sh
batch-flash.sh		batch-flash.sh
batch-gatk-FasAltRefMaker-gma.sh		batch-gatk-FasAltRefMaker-gma.sh
batch-genomcov.sh		batch-genomcov.sh
batch-gff2gtf.sh		batch-gff2gtf.sh
batch-hisat2-fq-paired-20%SNP.sh		batch-hisat2-fq-paired-20%SNP.sh
batch-hisat2-fq-paired-cyp.sh		batch-hisat2-fq-paired-cyp.sh
batch-hisat2-fq-paired-eas.sh		batch-hisat2-fq-paired-eas.sh
batch-hisat2-fq-paired-flexible.sh		batch-hisat2-fq-paired-flexible.sh
batch-hisat2-fq-paired_no_dedup.sh		batch-hisat2-fq-paired_no_dedup.sh
batch-hisat2-fq-paired_with_dedup.sh		batch-hisat2-fq-paired_with_dedup.sh
batch-hisat2-fq-single-20%SNP.sh		batch-hisat2-fq-single-20%SNP.sh
batch-hisat2-fq-single-cyp.sh		batch-hisat2-fq-single-cyp.sh
batch-hisat2-fq-single_dedup.sh		batch-hisat2-fq-single_dedup.sh
batch-parse-uniprot_nhr.sh		batch-parse-uniprot_nhr.sh
batch-pull_contigs.sh		batch-pull_contigs.sh
batch-segemehl-index.sh		batch-segemehl-index.sh
batch-segemehl-pe-cyp.sh		batch-segemehl-pe-cyp.sh
batch-star-single.sh		batch-star-single.sh
batch-star-test.sh		batch-star-test.sh
batch-transpose_012matrix.sh		batch-transpose_012matrix.sh
batch-trimmomatic-pe.sh		batch-trimmomatic-pe.sh
batch-trimmomatic-se-eas.sh		batch-trimmomatic-se-eas.sh
batch-trimmomatic-se.sh		batch-trimmomatic-se.sh
batch_avg-gencov-summary.sh		batch_avg-gencov-summary.sh
bcftools-consensus.sh		bcftools-consensus.sh
bcftools_parallel_eas-edited.sh		bcftools_parallel_eas-edited.sh
bcftools_parallel_eas.sh		bcftools_parallel_eas.sh
blastn-mod.sh		blastn-mod.sh
blastn-sharks.sh		blastn-sharks.sh
blastn.sh		blastn.sh
blastp-uniprot_nhr.sh		blastp-uniprot_nhr.sh
blastx-uniprot_nhr.sh		blastx-uniprot_nhr.sh
blastx.sh		blastx.sh
bowtie2-paired-3snps.sh		bowtie2-paired-3snps.sh
bwa_rockfish.sh		bwa_rockfish.sh
cap3.sh		cap3.sh
clean_genemodels.py		clean_genemodels.py
clean_mapping_outs.sh		clean_mapping_outs.sh
consensus-contigs.sh		consensus-contigs.sh
db-to-db_unique_match.py		db-to-db_unique_match.py
ddocent-vcftools-snpfilter.sh		ddocent-vcftools-snpfilter.sh
example_Trinity_mkm.sbatch		example_Trinity_mkm.sbatch
extract-gms_from_exons.py		extract-gms_from_exons.py
extract_contig_by_name.py		extract_contig_by_name.py
extract_contigs.py		extract_contigs.py
extract_contigs_seqio-fast.py		extract_contigs_seqio-fast.py
extract_multiple_contigs_by_name.py		extract_multiple_contigs_by_name.py
extract_one_seq.py		extract_one_seq.py
extract_seqs.py		extract_seqs.py
fastVCFcombine.sh		fastVCFcombine.sh
fasta-blast_seq-name-mod.py		fasta-blast_seq-name-mod.py
filter-assembly.py		filter-assembly.py
gatk-consensus.sh		gatk-consensus.sh
genomecov-default.sh		genomecov-default.sh
genomecov2.sh		genomecov2.sh
get-bam-counts.sh		get-bam-counts.sh
get-orf-predictions.sh		get-orf-predictions.sh
get_unique_blasts.py		get_unique_blasts.py
gff2gtf.py		gff2gtf.py
gff3-fix.py		gff3-fix.py
good_conch_mplex_03052018.csv		good_conch_mplex_03052018.csv
good_conch_mplex_03052018_numeric.csv		good_conch_mplex_03052018_numeric.csv
hya-transcript-reference-maker.py		hya-transcript-reference-maker.py
longest-isoform.pl		longest-isoform.pl
make_gene_models.py		make_gene_models.py
make_gms_tenuis.py		make_gms_tenuis.py
match-aten2ahya-seqs.py		match-aten2ahya-seqs.py
merge_sort_bams.sh		merge_sort_bams.sh
mothur-taxa-summary.py		mothur-taxa-summary.py
parse-uniprot-xml_nhr.py		parse-uniprot-xml_nhr.py
peter_convert_accession-R.txt		peter_convert_accession-R.txt
plot.py		plot.py
prevent_deletion.sh		prevent_deletion.sh
pull_scaffolds.py		pull_scaffolds.py
remove_last_line.sh		remove_last_line.sh
scaf_lengths.py		scaf_lengths.py

Repository files navigation

Scripts for processing genomic data

These scripts are routinely used by the Palumbi lab @hopkinsmarinestation to process and analyze genomic data. Please note that some scripts are not optimized for best time or space complexity.

Contact

Suggestions to make these scripts better are welcome! For questions or suggested edits, please contact the repository owner @ [cypayne at stanford dot edu]

cypayne/palumbi_scripts

Folders and files

Latest commit

History