1. Assess the assembly

seqfu stats -b --gc --index contigs.fa

File	#Seq	Total bp	Avg	N50	N75	N90	auN	Min	Max	%GC	L50	L75	L90
contigs	40	34563	864.08	1522	513	397	2547.14	208	7585	0.46	6	19	30

--index adds the L50/L75/L90 contig counts and --gc the GC content.

2. Filter by length and coverage

Assemblers such as SPAdes, MEGAHIT, Unicycler and Shovill write the coverage of each contig in its name. fu-cov reads it and filters on it:

fu-cov -c 10 -l 500 contigs.fa > filtered.fa

9/40 sequences printed (40 with coverage info) from 1 files.
Skipped:          2 too short, 0 too long, then 29 low coverage, 0 high coverage, .
Total size:       10258/34563 bp printed (29.7%)

fu-cov -s -t 10 contigs.fa prints the ten contigs with the highest coverage instead.

3. Rename the contigs

Many downstream tools prefer short, simple names. seqfu cat replaces the name with a prefix and a zero-padded counter, drops the comments, and can save the old-to-new mapping:

seqfu cat -z -p ctg --zero-pad 4 -s --report rename.tsv filtered.fa > final.fa
head -n 1 final.fa

>ctg0001

For anvi’o, seqfu cat --anvio applies its naming rules in one go.