(Nucleomics-VIB)
- NGS-Tools
All tools presented below have only been tested by me and may contain bugs, please let me know if you find some. Each tool relies on dependencies normally listed at the top of the code (cpan for perl, R packages, etc.)
Please refer to the accompanying wiki for examples and workflows.
The perl script fastastats.pl computes simple length statistics on a multi-fasta file.
## Usage: fastastats.pl <-i fasta-file (can be compressed)>
# Additional optional filtering parameters are:
# <-m minsize in kb (0)>
# <-x maxsize in kb (1E+6 | 1Gb)>
# <-h to display this help>The perl script fastaCleanHeader.pl cleans complex fasta record names that may interfere with some applications.
## Usage: fastaCleanHeader.pl <-i fasta_file (required)>
# <-o output file name (default to "cleaned_"<infile>; optional)>
# <-c keep only the leftmost word (display_id field; optional)>
# <-d delimiter (default to '|'; optional)>
# <-z to compress results with bgzip>
# <-h to display this help>The perl script fasta2merge.pl creates a single fasta sequence from a multifasta file (required for ABACAS -r ref.fasta).
## Usage: fasta2merge.pl <-i fasta-file>
# script version 1.0, 2017_09_05
# Additional optional parameters are:
# <-o prefix for output (default to merged-<inputname>.fasta)>
# <-h to display this help>The perl script fastabreak.pl breaks a multifasta file into individual fasta files.
## Usage: fastabreak.pl <-i fasta-file>
# script version 1.0, 2017_09_05
# Additional optional parameters are:
# <-o output directory (default to current directory)>
# <-h to display this help>The perl script fastarotate.pl rotates sequences in a fasta file.
## Usage: fastarotate.pl <-i fasta-file>
# script version 1.0, 2017_09_05
# Additional optional parameters are:
# <-o output file (default to rotated_<inputname>.fasta)>
# <-h to display this help>The perl script fastaSplit.pl splits a multifasta file into smaller files.
## Usage: fastaSplit.pl <-i fasta-file>
# script version 1.0, 2017_09_05
# Additional optional parameters are:
# <-o output prefix (default to split_<inputname>)>
# <-n number of sequences per file (default to 1)>
# <-h to display this help>The bash script fasta2consensus.sh generates a consensus sequence from a multifasta file.
# Usage: fasta2consensus.sh -i <fasta file>
# script version 1.0, 2025_03_14
# [optional: -o <output file>]
# [optional: -h <this help text>]The bash script fastp_benchmark.sh benchmarks fastp for fastq file processing.
# Usage: fastp_benchmark.sh -i <fastq file>
# script version 1.0, 2025_03_14
# [optional: -o <output directory>]
# [optional: -t <number of threads>]
# [optional: -h <this help text>]The bash script run_Hifiasm_meta.sh processes PacBio HiFi data through conversion (if needed) and assembly.
# Usage: run_Hifiasm_meta.sh [-q] [-b INPUT_BAM_DIR] [-f FASTQ_DIR] [-o OUTPUT_ASM_DIR] [-n THREADS] [-j MAX_JOBS] [-t ASM_THREADS]
# script version 1.0, 2025_03_14
# Options:
# -q start directly from FASTQ files (default: process BAM files)
# -b DIR input BAM directory (default: bam_data)
# -f DIR FASTQ input/output directory (default: fastq_data)
# -o DIR assembly output directory (default: asm_results)
# -n INT threads for bam2fastq (default: 4)
# -j INT max concurrent jobs (default: 4)
# -t INT threads per hifiasm_meta (default: 20)The bash script run_freebayes.sh calls variants with freebayes from mappings and a reference genome.
# Usage: run_freebayes.sh -i <bam file> -r <fasta reference>
# script version 1.0, 2016_09_28
# [optional: -m <minmapq|20>]
# [optional: -q <minbaseq|20>]
# [optional: -F <minaltfrac|0.01>]
# [optional: -C <minaltcnt|10>]The bash script makeENSref.sh creates a series of reference files from ENSembl FTP downloads.
# Usage: makeENSref.sh
# -o <organism (default to <homo_sapiens>)>
# -b <build number (default to <GRCh38>)>
# -r <release number (default to 88)>
# script version 1.0, 2017_04_05
# [-h for this help]The bash script gepard_plot.sh creates a xy-plot from two related assemblies. The Java GUI tools does the same but this script is applicable to multiple inputs in batch. The original tool can be found at https://github.com/univieCUBE/gepard.
# Usage: gepard_plot.sh -x <reference assembly> -y <draft assembly> -p <path to gepard.jar and matrices>
# script version 1.1, 2017_09_05
# [optional: -o <result path/prefix>]
# [optional: -w <word size:10>]
# [optional: -W <window size:0>]
# [optional: -l <lower value% (default:0)>]
# [optional: -u <upper value% (default:100)>]
# [optional: -g <greyscale start value% (default:0)>]
# [optional: -J <java extra parameters (eg -Xmx1G, put between double quotes if it contains spaces)>
# [optional: -h <this help text>]The bash script mauve_reorder.sh reorders a draft-assembly based on a reference assembly at CLI. The Java GUI tools does the same but this script is applicable to multiple inputs in batch. The original tool can be found at http://darlinglab.org/mauve/download.html
# Usage: mauve_reorder.sh -i <draft assembly> -r <reference assembly> -p <mauve path>
# script version 1.0, 2017_04_21
# [optional: -o <result folder>]
# [optional: -m <available RAM|1G>]
# [optional: -h <this help text>]The bash script mappability.sh creates a mappability track for a given single-read length and a reference genome. Such tracks used to be present in IGV from the web server and have been removed. A mappability track allows you to identify those regions of the genome which are so ubiquitous that reads have no chance to map to them and explain why you may not observe coverage in these regions (Derrien et al., 2012). For more info about this data type, please look at our page http://wiki.bits.vib.be/index.php/Create_a_mappability_track. The script depends on a number of resources including the gem-libraries and several of Jim Kent's Utilities KentUtils.
# Usage: mappability.sh
# -i <reference assembly fasta>)>
# -l <single read length for prediction (default to 100bps)>
# -p <prefix for output data (default to input file prefix)>
# -t <number of threads (default to 1)>
# script version 1.0, 2017_05_19
# [-h for this help]The bash script GATK_Variant_Analysis.sh performs variant analysis using GATK.
# Usage: GATK_Variant_Analysis.sh -i <input file> -r <reference genome>
# script version 1.0, 2025_03_14
# [optional: -o <output directory>]
# [optional: -t <number of threads>]
# [optional: -h <this help text>]The bash script run_Deepvariant.sh runs DeepVariant for variant calling.
# Usage: run_Deepvariant.sh -i <input file> -r <reference genome>
# script version 1.0, 2025_03_14
# [optional: -o <output directory>]
# [optional: -t <number of threads>]
# [optional: -h <this help text>]The bash script varscan2mpileup2cns.sh calls variants using Varscan2 and mpileup.
# Usage: varscan2mpileup2cns.sh -i <input file> -r <reference genome>
# script version 1.0, 2025_03_14
# [optional: -o <output directory>]
# [optional: -t <number of threads>]
# [optional: -h <this help text>]The bash script varscan2mpileup2somatic.sh calls somatic variants using Varscan2 and mpileup.
# Usage: varscan2mpileup2somatic.sh -i <input file> -r <reference genome>
# script version 1.0, 2025_03_14
# [optional: -o <output directory>]
# [optional: -t <number of threads>]
# [optional: -h <this help text>]The bash script varscan2mpileup2trio.sh calls trio variants using Varscan2 and mpileup.
# Usage: varscan2mpileup2trio.sh -i <input file> -r <reference genome>
# script version 1.0, 2025_03_14
# [optional: -o <output directory>]
# [optional: -t <number of threads>]
# [optional: -h <this help text>]The bash script asm2cvg.sh computes coverage from an assembly file.
# Usage: asm2cvg.sh -i <assembly file>
# script version 1.0, 2025_03_14
# [optional: -o <output file>]
# [optional: -h <this help text>]The bash script asm2dotplot.sh creates a dot plot from an assembly file.
# Usage: asm2dotplot.sh -i <assembly file>
# script version 1.0, 2025_03_14
# [optional: -o <output file>]
# [optional: -h <this help text>]The bash script bcftoolsParallel.sh runs bcftools in parallel.
# Usage: bcftoolsParallel.sh -i <input file>
# script version 1.0, 2025_03_14
# [optional: -o <output directory>]
# [optional: -t <number of threads>]
# [optional: -h <this help text>]The bash script bed2density.sh converts a BED file to a density file.
# Usage: bed2density.sh -i <BED file>
# script version 1.0, 2025_03_14
# [optional: -o <output file>]
# [optional: -h <this help text>]The bash script blast_assembly2NT.sh performs BLAST on an assembly against the NT database.
# Usage: blast_assembly2NT.sh -i <assembly file>
# script version 1.0, 2025_03_14
# [optional: -o <output directory>]
# [optional: -t <number of threads>]
# [optional: -h <this help text>]The perl script circ-perm.pl performs circular permutation on sequences.
## Usage: circ-perm.pl <-i input file>
# script version 1.0, 2025_03_14
# Additional optional parameters are:
# <-o output file (default to circ_perm_<inputname>.txt)>
# <-h to display this help>The bash script cmpasm2vcf.sh compares assemblies and generates a VCF file.
# Usage: cmpasm2vcf.sh -i <input file>
# script version 1.0, 2025_03_14
# [optional: -o <output file>]
# [optional: -h <this help text>]The bash script compare_all2all.sh compares all sequences to all other sequences.
# Usage: compare_all2all.sh -i <input file>
# script version 1.0, 2025_03_14
# [optional: -o <output file>]
# [optional: -h <this help text>]The bash script consensusQualFilter.sh filters consensus sequences based on quality.
# Usage: consensusQualFilter.sh -i <input file>
# script version 1.0, 2025_03_14
# [optional: -o <output directory>]
# [optional: -t <number of threads>]
# [optional: -h <this help text>]The bash script create_xenome-idx_all.sh creates Xenome indices for all input files.
# Usage: create_xenome-idx_all.sh -i <input file>
# script version 1.0, 2025_03_14
# [optional: -o <output directory>]
# [optional: -t <number of threads>]
# [optional: -h <this help text>]The bash script DownsampleBam_x.sh downsamples BAM files.
# Usage: DownsampleBam_x.sh -i <input file>
# script version 1.0, 2025_03_14
# [optional: -o <output directory>]
# [optional: -t <number of threads>]
# [optional: -h <this help text>]The awk script fastq2metrics.awk calculates metrics from a fastq file.
# Usage: fastq2metrics.awk -i <fastq file>
# script version 1.0, 2025_03_14
# [optional: -o <output file>]
# [optional: -h <this help text>]The C++ script fastq2metrics.cpp calculates metrics from a fastq file.
# Usage: fastq2metrics.cpp -i <fastq file>
# script version 1.0, 2025_03_14
# [optional: -o <output file>]
# [optional: -h <this help text>]The C++ script fastq2metrics60.cpp calculates metrics from a fastq file.
# Usage: fastq2metrics60.cpp -i <fastq file>
# script version 1.0, 2025_03_14
# [optional: -o <output file>]
# [optional: -h <this help text>]The python script fastq2motif.py identifies motifs in fastq sequences.
# Usage: fastq2motif.py -i <fastq file>
# script version 1.0, 2025_03_14
# [optional: -o <output file>]
# [optional: -h <this help text>]