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IDBA_TRAN(1) User Commands IDBA_TRAN(1)


idba_tran - Iterative de Bruijn Graph Assembler for hybrid sequencing data


idba_tran -r read.fa -o output_dir


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

Allowed Options:

-o, --out arg (=out)
output directory
-r, --read arg
fasta read file (<=128)
-l, --long_read arg
fasta long read file (>128)
--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
do not use local assembly
do not iterate on coverage
do not do correction
perform pre-correction before assembly
--max_isoforms arg (=3)
maximum number of isoforms
--max_component_size arg (=30)
maximum size of components
August 2017 idba_tran 1.1.3