Seqkit is a suite of software utilities for manipulating and analyzing common genome sequencing data types (FASTA, SAM). Seqkit is written in Rust, and uses rust-htslib for reading and writing BAM files. Seqkit is divided into two utilities: fasta and sam. Each utility provides various useful subcommands. For a complete listing type the command name without arguments into your shell.
For FASTA/FASTQ files, Seqkit can:
- Convert between FASTA, FASTQ and raw sequence-per-line formats
- Extract sample barcodes and UMIs from multiplexed FASTQ sequencing data
- Demultiplex FASTQ sequencing data
- Trim FASTQ sequencing data by per-base quality (BASEQ) values
- Mask low quality bases in FASTQ sequencing data
- Replace FASTQ read identifiers with compact numeric IDs
For BAM files, Seqkit can:
- Extract reads from name-sorted or position-sorted BAM files
- Calculate a histogram of fragment lengths
- Calculate statistics about unaligned, aligned and duplicate-flagged reads
Install Rust (version 1.31 or later). Then run the following command:
cargo install --git https://github.com/annalam/seqkit
Extract reads from a name-sorted or position-sorted BAM file called tumor.bam. Paired end reads are written in gzip-compressed FASTQ format into output files tumor_1.fq.gz and tumor_2.fq.gz, which are automatically created. Orphan reads are written into output file tumor.fq.gz. The second parameter specifies the prefix used for the output file names.
sam to fastq tumor.bam tumor
Extract UMIs and demultiplex Illumina sequencing data where both the sample barcode and UMI are stored in the adapter:
fasta demultiplex sample_sheet.tsv
<(fasta add barcode multiplexed_R1.fq.gz multiplexed_I1.fq.gz)
<(fasta add barcode multiplexed_R2.fq.gz multiplexed_I1.fq.gz)