Inspect a new sequencing run A first look at a directory of FASTQ files - integrity, read counts, lengths and quality encoding. seqfu checkseqfu countseqfu statsseqfu qualseqfu view Prepare and validate a sample sheet Generate a metadata or manifest file from a directory of reads and validate it before running a pipeline. seqfu metadataseqfu tabcheckseqfu check Merge lanes per sample Combine the L001-L004 files produced by an Illumina run into one R1 and one R2 file per sample. seqfu lanesseqfu count Dereplicate amplicon reads Collapse identical sequences, keep their abundance, and carry the counts across multiple rounds of dereplication. seqfu derepseqfu sortseqfu statsseqfu grep Extract reads by a list of IDs Pull out (or remove) the records named in a list, keeping paired-end files in sync. seqfu listseqfu by-idseqfu subtractseqfu count Filter and rename an assembly Assess an assembly, drop short or low-coverage contigs, and give the survivors clean names. seqfu statsfu-covseqfu cat

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