ngsutilsj is an updated java port of the NGSUtils toolkit. This new version is largely a Java port of the the most commonly used tools from NGSUtils, with some additions thrown in. It is also a library, with utility classes for use in other various NGS related software (such as cgsplice).
Java was chosen for the ease of installation and relative speed (in comparison to the Python NGSUtils). The processing speed for gzipped compressed files was a major reason for the new update. This version has also been optimized for working on high-memory HPC clusters and streaming data analysis (to minimize disk IO).
ngsutilsj is distributed as a self-executing fat-JAR file. This means that for installation, all one needs is a working copy of Java and the
ngsutilsj file. Unlike other JAR-file based NGS packages, ngsutilsj includes a shell script shim to make it executable like a traditional Unix program. This means that to install the program, you need to copy the
ngsutilsj file to somewhere in your
There are many commands available. For information on an individual command, run
ngsutilsj help command
ngsutilsj - Data wrangling for NGS --------------------------------------- Usage: ngsutilsj cmd [options] Available commands: [bam] bam-basecall - For a BAM file, output the basecalls (ACGTN) at each genomic position. bam-best - With reads mapped to two bam references, determine which reads mapped best to each bam-bins - Quickly count the number of reads that fall into bins (bins assigned based on 5' end of the first read) bam-check - Checks a BAM file to make sure it is valid bam-concat - Concatenates BAM files (handles @RG, @PG) bam-count - Counts the number of reads for genes (GTF), within a BED region, or by bins (--gtf, --bed, or --bins required) bam-coverage* - Scans an aligned BAM file and calculates the number of reads covering each base bam-discord - Extract all discordant reads from a BAM file bam-dups - Flags or removes duplicate reads bam-expressed - For a BAM file, output all regions with significant coverage in BED format. bam-filter - Filters out reads based upon various criteria bam-readgroup - Add a read group ID to each read in a BAM file bam-sample* - Create a whitelist of read names sampled randomly from a file bam-split - Split a BAM file into smaller files bam-stats - Stats about a BAM file and the library orientation bam-tobed* - Writes read positions to a BED6 file bam-tobedgraph - Calculate coverave for an aligned BAM file in BedGraph format. bam-tofastq - Export the read sequences from a BAM file in FASTQ format [bed] bed-clean - Cleans score entries to be an integer bed-count - Given reference and query BED files, count the number of query regions that are contained within each reference region bed-nearest - Given reference and query BED files, for each query region, find the nearest reference region bed-reduce - Merge overlaping BED regions bed-resize - Resize BED regions (extend or shrink) bed-tobed3 - Convert a BED3+ file to a strict BED3 file bed-tobed6 - Convert a BED6+ file to a strict BED6 file bed-tofasta - Extract FASTA sequences based on BED coordinates [fasta] fasta-filter - Filter out sequences from a FASTA file fasta-gc - Determine the GC% for a given region or bins fasta-genreads* - Generate mock reads from a reference FASTA file fasta-mask - Mask regions of a FASTA reference fasta-names - Display sequence names from a FASTA file fasta-split - Split a FASTA file into a new file for each sequence present fasta-subseq - Extract subsequences from a FASTA file (optionally, indexed) fasta-tag - Add prefix/suffix to FASTA sequence names fasta-wrap - Change the sequence wrapping length of a FASTA file [fastq] fastq-barcode - Given Illumina 1.8+ naming, find the lane/barcodes included fastq-check - Verify a FASTQ single, paired, or interleaved file(s) fastq-demux - Splits a FASTQ file based on lane/barcode values fastq-filter - Filters reads from a FASTQ file. fastq-merge - Merges two FASTQ files (R1/R2) into one interleaved file. fastq-separate - Splits an interleaved FASTQ file by read number. fastq-sort - Sorts a FASTQ file fastq-split - Splits an FASTQ file into smaller files fastq-stats - Statistics about a FASTQ file fastq-tobam - Converts a FASTQ file (or two paired files) into an unmapped BAM file fastq-tofasta - Convert FASTQ sequences to FASTA format [gtf] gtf-export - Export gene annotations from a GTF file as BED regions gtf-geneinfo* - Calculate information about genes (based on GTF model) [annotation] annotate-gtf - Annotate GTF gene regions (for tab-delimited text, BED, or BAM input) annotate-repeat* - Calculates Repeat masker annotations [vcf] vcf-annotate - Annotate a VCF file vcf-chrfix - Changes the reference (chrom) format (Ensembl/UCSC) vcf-export - Export information from a VCF file vcf-filter - Filter a VCF file vcf-tobed - Export allele positions from a VCF file to BED format [help] help - Help for a specific command license - Show the license * = experimental command