Tools

fu-msa wrapperdeprecated Legacy launcher for seqfu msa (prints a migration notice first). AlignmentFASTA↔ seqfu msa seqfu head Print the first sequences of one or more files, optionally sampling one every N. FASTAFASTQ seqfu less interactive Interactive full-screen pager for FASTA/FASTQ files, like less for sequences. FASTAFASTQ seqfu msa experimentalinteractive Interactive viewer for multiple sequence alignments in the terminal. AlignmentFASTA↔ fu-msa seqfu tail Print the last sequences of one or more files. FASTAFASTQ seqfu view Display sequences with colour-coded quality bars and highlighted oligo matches. FASTAFASTQ

fu-index Report the Illumina index (barcode) found in the headers of FASTQ files. FASTQ fu-pecheck experimentalpython Check the integrity of paired-end FASTQ files in a directory. Directory seqfu amplicheck QC single- or paired-end amplicon FASTQ files and suggest DADA2-style trimming parameters. FASTQ seqfu bases Report base composition and %GC content of FASTA/FASTQ files. FASTAFASTQ seqfu check experimental Check the integrity of FASTQ files, pairs or whole directories. FASTQDirectory seqfu count Count sequences in FASTA/FASTQ files, pairing R1/R2 automatically. FASTAFASTQ seqfu qual Detect the quality encoding and profile per-position quality scores. FASTQ seqfu stats Report counts, total length, N50, auN and other assembly metrics per file. FASTAFASTQ

fu-cov Filter assembly contigs by length and by the coverage stored in their names. FASTA fu-primers Remove amplification primers from single- or paired-end amplicon reads. FASTQ fu-virfilter Filter sequences using a VirFinder predictions table. FASTATSV-CSV seqfu by-comment Select records by comment text or typed key=value attributes and expressions. FASTAFASTQ seqfu by-id Select records by identifier, with patterns, lists and numeric-suffix ranges. FASTAFASTQ seqfu by-seq Select records by biological sequence using IUPAC patterns, mismatches and strands. FASTAFASTQ seqfu derep Dereplicate sequences, keeping the number of identical copies in the header. FASTAFASTQ seqfu grep Select sequences by name, comment or oligonucleotide match, allowing mismatches. FASTAFASTQ seqfu list Extract sequences whose names appear in one or more list files. FASTAFASTQ seqfu subtract Print sequences from a first file that are absent from a second file. FASTAFASTQ seqfu trim Quality-trim and filter single- or paired-end FASTQ files. FASTQ

fu-multirelabel Relabel sequences across multiple files, ensuring unique names. FASTAFASTQ fu-shred wrapperdeprecated Deprecated launcher that forwards its arguments to seqfu shred. FASTAFASTQ↔ seqfu shred fu-split experimentalpython Split a FASTA/FASTQ file into chunks by files, sequences or bases. FASTAFASTQ seqfu cat Concatenate FASTA/FASTQ files, renaming, annotating and filtering records on the way. FASTAFASTQ seqfu homocomp Collapse homopolymer runs in FASTA/FASTQ records. FASTAFASTQ seqfu rc Reverse-complement sequence files or IUPAC strings given on the command line. FASTAFASTQ seqfu rotate Rotate (restart) sequences at a new position or at a motif. FASTAFASTQ seqfu shred Systematically tile sequences into single- or paired-end reads. FASTAFASTQ↔ fu-shred seqfu sort Sort sequences by length, removing duplicates across all input files. FASTA seqfu tofasta Convert GenBank, EMBL, GFF, GFA, alignments and FASTQ to FASTA. FASTAFASTQAlignmentGenBankGFFGFA

seqfu deinterleave Split an interleaved FASTQ file into separate R1 and R2 files. FASTQ seqfu interleave Interleave paired-end reads from two FASTQ files into one stream. FASTQ seqfu lanes Merge Illumina lanes (L001, L002...) into one file per sample. Directory seqfu merge experimental Merge overlapping paired-end reads into single fragments. FASTQ

fu-tabcheck wrapper Compatibility wrapper for seqfu tabcheck. TSV-CSV↔ seqfu tabcheck seqfu metadata Generate sample sheets and mapping files from directories of reads. Directory seqfu tabcheck Validate TSV/CSV files for consistent column counts, and inspect column types. TSV-CSV↔ fu-tabcheck seqfu tabulate Convert FASTA/FASTQ to a tabular format and back, for line-based processing. FASTAFASTQTSV-CSV

fu-16Sregion experimental Detect the 16S hypervariable region(s) covered by amplicon reads. FASTAFASTQ fu-nanotags experimental Search for tags in long reads with Smith-Waterman alignment. FASTQ fu-orf wrapper Compatibility wrapper for seqfu orf. FASTAFASTQ↔ seqfu orf fu-sw Align query sequences against a target with Smith-Waterman local alignment. FASTAFASTQ seqfu orf Extract open reading frames from nucleotide sequences or read pairs. FASTAFASTQ↔ fu-orf