idba_tran1

Iterative de bruijn graph assembler for next-generation transcriptome sequencing data.

Usage

idba_tran -r read.fa -o output_dir

IDBA-Tran - Iterative de Bruijn Graph Assembler for next-generation transcriptome sequencing data.

`--mink arg (=20)`	minimum k value (<=124)
`--maxk arg (=60)`	maximum k value (<=124)
`--step arg (=10)`	increment of k-mer of each iteration
`--inner_mink arg (=10)`	inner minimum k value
`--inner_step arg (=5)`	inner increment of k-mer
`--prefix arg (=3)`	prefix length used to build sub k-mer table
`--min_count arg (=2)`	minimum multiplicity for filtering k-mer when building the graph
`--min_support arg (=1)`	minimum supoort in each iteration
`--num_threads arg (=0)`	number of threads
`--seed_kmer arg (=30)`	seed kmer size for alignment
`--min_contig arg (=200)`	minimum size of contig
`--min_transcript arg (=300)`	minimum size of transcript
`--similar arg (=0.95)`	similarity for alignment
`--max_mismatch arg (=3)`	max mismatch of error correction

`--max_isoforms arg (=3)`	maximum number of isoforms
`--max_component_size arg (=30)`	maximum size of components

4 releases since Debian 10 (Buster); the text changed 1 time.