Alternatives to SeqKit
A command-line toolkit for inspecting, filtering, transforming, and converting FASTA and FASTQ files. Notes say what changes if you switch.
The original
SeqKit
A command-line toolkit for inspecting, filtering, transforming, and converting FASTA and FASTQ files.
10 alternatives
Most similar to SeqKit first.
Seqtk
A command-line toolkit for processing FASTA and FASTQ sequencing files.
Seqtk also processes FASTA and FASTQ files from the command line, but offers a narrower toolkit than SeqKit's inspection and conversion features.
Sambamba
A command-line toolkit for filtering, sorting, indexing and managing SAM and BAM sequencing files.
fastp
A command-line tool that preprocesses and checks quality of short-read FASTQ sequencing data.
RustQC
RustQC provides command-line quality control analyses for sequencing alignment files.
Picard
A Java command-line toolkit for manipulating high-throughput sequencing data and file formats.
Trim Galore
A command-line tool for trimming adapters and low-quality regions from next-generation sequencing reads.
fastplong
A command-line tool for preprocessing and quality control of long-read sequencing data.
Cutadapt
A command-line tool for trimming adapters, primers, and other unwanted sequences from sequencing reads.
mosdepth
A command-line tool for calculating sequencing coverage depth from BAM and CRAM files.
Samtools
A command-line suite for reading, writing, editing and indexing sequencing data files.
Samtools handles sequencing data files from the command line, while SeqKit focuses on inspecting, filtering and converting FASTA and FASTQ.
