genomics-bcftbx
stable
Installation and set up
Usage
Command Reference
Genome indexes and reference data utilities
SOLiD data handling utilities
Illumina data handling utilities
General NGS utilities
ChIP-seq specific utilities
RNA-seq specific utilities
QC utilities
Microarray utilities
General non-bioinformatic utilities
bcftbx
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genomics-bcftbx
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Command Reference
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Command Reference
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Genome indexes and reference data utilities
fetch_fasta.sh
build_indexes.sh
bfast_build_indexes.sh
bowtie_build_indexes.sh
bowtie2_build_indexes.sh
srma_build_indexes.sh
index_indexes.sh
setup_genome_indexes.sh
build_rRNA_bowtie_indexes.sh
make_seq_alignments.sh
SOLiD data handling utilities
rsync_solid_to_cluster.sh
log_seq_data.sh
analyse_solid_run.py
build_analysis_dir.py
Illumina data handling utilities
analyse_illumina_run.py
auto_process_illumina.sh
bclToFastq.sh
build_illumina_analysis_dirs.py
demultiplex_undetermined_fastq.py
prep_sample_sheet.py
report_barcodes.py
rsync_seq_data.py
verify_paired.py
General NGS utilities
explain_sam_flag.sh
extract_reads.py
fastq_edit.py
fastq_sniffer.py
SamStats
splitBarcodes.pl
remove_mispairs.pl
remove_mispairs.py
reorder_fasta.py
sam2soap.py
separate_paired_fastq.pl
split_fasta.py
split_fastq
trim_fastq.pl
uncompress_fastqgz.sh
ChIP-seq specific utilities
calc_coverage_stats.pl
convertFastq2Fasta.pl
CreateChIPalignFileFromBed.pl
getRandomTags_index.pl, getRandomTags_index_fastq.pl
make_macs2_xls.py
mean_coverage.pl
run_DESeq.R
RNA-seq specific utilities
bowtie_mapping_stats.py
GFFedit
qc_bash_script.sh
Split
QC utilities
run_qc_pipeline.py
illumina_qc.sh
qcreporter.py
fastq_screen.sh
qc_boxplotter
boxplotps2png.sh
solid_preprocess_filter.sh
solid_preprocess_truncation_filter.sh
fastq_strand.py
Microarray utilities
annotate_probesets.py
best_exons.py
xrorthologs.py
General non-bioinformatic utilities
cd_set_umask.sh
do.sh
cmpdirs.py
cluster_load.py
makeBinsFromBed.pl
makeRegularBinsFromGenomeTable.R
make_mock_solid_dir.py
manage_seqs.py
md5checker.py
symlink_checker.py
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