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fefe_greening
fefe_greening
 
 
scgs
scgs
 
 
.gitignore
.gitignore
 
 
16S_bins.py
16S_bins.py
 
 
ANI.sh
ANI.sh
 
 
LICENSE.md
LICENSE.md
 
 
README.md
README.md
 
 
abundance_sort.py
abundance_sort.py
 
 
app_each_line.py
app_each_line.py
 
 
assign2bin.py
assign2bin.py
 
 
bin_scaffolds_by_tsv.py
bin_scaffolds_by_tsv.py
 
 
biotite_config.py
biotite_config.py
 
 
bootTree.py
bootTree.py
 
 
borehole_map_biotite.py
borehole_map_biotite.py
 
 
breseq_promoters.py
breseq_promoters.py
 
 
build_connection_graph.py
build_connection_graph.py
 
 
build_toc.py
build_toc.py
 
 
build_tree-1.py
build_tree-1.py
 
 
build_tree-2.py
build_tree-2.py
 
 
build_tree-3.py
build_tree-3.py
 
 
changeFastaHeader.py
changeFastaHeader.py
 
 
class2fasta.py
class2fasta.py
 
 
class_wrapper.py
class_wrapper.py
 
 
cls_to_tsv.py
cls_to_tsv.py
 
 
cluster_coverage.py
cluster_coverage.py
 
 
common_objects.py
common_objects.py
 
 
compare_blasts.py
compare_blasts.py
 
 
coverage2avg.py
coverage2avg.py
 
 
crispr_parser.py
crispr_parser.py
 
 
csvRepair.sh
csvRepair.sh
 
 
efetch.py
efetch.py
 
 
fasta_features.py
fasta_features.py
 
 
fasta_reformat.py
fasta_reformat.py
 
 
fix_gff3.py
fix_gff3.py
 
 
fix_header.py
fix_header.py
 
 
freebayes_snps.py
freebayes_snps.py
 
 
gene2scaffold
gene2scaffold
 
 
generateNs.py
generateNs.py
 
 
grep_scaffolds.py
grep_scaffolds.py
 
 
histogram.py
histogram.py
 
 
kcmgr.py
kcmgr.py
 
 
kegg_hmms.tar.gz
kegg_hmms.tar.gz
 
 
leveldb_wrapper.py
leveldb_wrapper.py
 
 
leveldbmgr.py
leveldbmgr.py
 
 
maxbinscafs.sh
maxbinscafs.sh
 
 
metabatscafs.sh
metabatscafs.sh
 
 
motif_search.py
motif_search.py
 
 
multi2single.py
multi2single.py
 
 
myblast.py
myblast.py
 
 
myusearch.py
myusearch.py
 
 
new_cluster.py
new_cluster.py
 
 
parse_breseq.py
parse_breseq.py
 
 
process_ani.py
process_ani.py
 
 
process_nodes.py
process_nodes.py
 
 
pullscaffolds.py
pullscaffolds.py
 
 
pysam_mismatched.py
pysam_mismatched.py
 
 
read_seq.py
read_seq.py
 
 
recluster_column.py
recluster_column.py
 
 
ref2tab.py
ref2tab.py
 
 
reformat_ggkb_proteins.py
reformat_ggkb_proteins.py
 
 
retrieve_annotations.py
retrieve_annotations.py
 
 
retrieve_ribosomal.py
retrieve_ribosomal.py
 
 
rewrite_contigs.py
rewrite_contigs.py
 
 
rib_prots.json
rib_prots.json
 
 
sam_header.py
sam_header.py
 
 
sam_reads.py
sam_reads.py
 
 
sam_slicer.sh
sam_slicer.sh
 
 
scg.py
scg.py
 
 
select_bases.py
select_bases.py
 
 
shannon_diversity.py
shannon_diversity.py
 
 
simple_kchash.c
simple_kchash.c
 
 
simple_kchash.py
simple_kchash.py
 
 
simplify_vcf.py
simplify_vcf.py
 
 
simpson_diversity.py
simpson_diversity.py
 
 
split_bins.py
split_bins.py
 
 
split_ggkbase_taxonomy_strings.py
split_ggkbase_taxonomy_strings.py
 
 
tapkee.py
tapkee.py
 
 
taxo_table_parser.py
taxo_table_parser.py
 
 
template.py
template.py
 
 
tests.py
tests.py
 
 
tot-bp
tot-bp
 
 
trimstring
trimstring
 
 
trna_check.py
trna_check.py
 
 
tsv_clustering.py
tsv_clustering.py
 
 
uniquify_fasta.py
uniquify_fasta.py
 
 
vcf_snps.py
vcf_snps.py
 
 

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These are some simple scripts I've developed (mainly in Python) for bioinformatics. Feel free to contact me with any questions you may have regarding usage or project ideas.

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