Releases
IDBA 0.20 Release on Jan 14,2011
IDBA tool kit 0.20 for 64-bit Linux. Add a script to performa T-IDBA (multiple-k).
Usage for T-IDBA (multiple-k)
script/tidba-multiple-k prefix read-file
Please install cd-hit-est before using this script. The output file can be found in prefix-cluster.fa.
IDBA 0.19 Release on Jan 14,2011
IDBA tool kit 0.19 for 64-bit Linux. Add Meta-IDBA(Iterative de Bruijn Graph De Novo short read Assembler for Metagenomics based on graph partition) into the toolkit. Please see more information in Meta-IDBA page.
Usage for Meta-IDBA
Meta-IDBA: Iterative De Bruijn graph short read Assembler for Metagenomics based on graph partition.
metaidba --read read-file [--output out] [options]
Allowed Options:
-h, --help produce help message
-r, --read arg read file
-l, --long arg long read file
-o, --output arg (=out) prefix of output
--mink arg (=25) minimum k value
--maxk arg (=50) maximum k value
--minCount arg (=2) filtering threshold for each k-mer
--cover arg (=0) the cutting coverage for contigs
--connect use paired-end reads to connect components
--minPairs arg (=5) minimum number of pair-end connections to join two components
--prefixLength arg (=3) length of the prefix of k-mer used to split k-mer table
The output consensus and alignment can be found in out.consensus and out.alignment.
Example
$ bin/metaidba --read meta-reads.fa --output out --connect
IDBA 0.18 Release on Oct 21,2010
IDBA tool kit 0.18 for 64-bit Linux. Add T-IDBA(Iterative de Bruijn Graph De Novo short read Assembler for Transcriptome) into the toolkit. Please see more information in T-IDBA page.
Usage for T-IDBA
T-IDBA: Iterative De Bruijn graph short read Assembler for transcriptome
tidba --read read-file [--output out] [options]
Allowed Options:
-h, --help produce help message
-r, --read arg read file
-o, --output arg (=out) prefix of output
--mink arg (=25) minimum k value
--modk arg (=50) moderate k value
--maxk arg (=90) maximum k value
--minCount arg (=2) filtering threshold for each k-mer
--minPairs arg (=5) minimum number of pair-end connections to join two contigs
--prefixLength arg (=3) length of the prefix of k-mer used to split k-mer table
The output isoforms can be found in out-isoforms.fa
Example
$ bin/tidba --read mouse-tran-reads.fa --output mouse
IDBA 0.17 Release on Aug 1,2010
IDBA tool kit 0.17 for 64-bit Linux. Remove boost requirement for installation this software.
Usage for IDBA tool kit for 64-bit Linux
idba --read read-file [--output out] [options]
Allowed options:
-h, --help produce help message
-r, --read arg read file
-l, --long arg long read file
-o, --output arg (=out) prefix of output
--scaffold use pair end information to merge contigs
--mink arg (=25) minimum k value
--maxk arg (=50) maximum k value
--minCount arg (=2) filtering threshold for each k-mer
--cover arg (=0) the cutting coverage for contigs
--minPairs arg (=5) minimum number of pair-end connections to join two contigs
--prefixLength arg (=3) length of the prefix of k-mer used to split k-mer table
The output contigs will be found in file out-contig.fa and out-contig-mate.fa. The former is single end output, the latter is pair end output. If you want to run pair-end version, please use --scaffold parameter.
Example (using the sample input)
$ bin/idba --read Lacto.reads-mate-30-0.01-75 --output lacto
If the data is in fastq format, please use fq2fa tool to do conversion first.
$ bin/fq2fa fq-file fa-file
IDBA(pair end) requires pair end reads stored in single file and a pair of reads is in consecutive two lines. If not, please use mergeReads to merge two read files to single file.
$ bin/mergeReads read-file1 read-file2 merge-read-file
Reads with same length are prefered. normReads tool can help to normlize reads. If the read-file is merged by mergeReads program, please use mate flag to do normalization.
$ bin/normReads read-file output-read-file --length l --mate
Installation Guide
Exract the package, then use make to compile the source code.
$ ./configure $ make
Sample Input and Output
Before your testing, please first read Installation Guide.
Simulated reads (30x depth, 75 read length, 1% error rate, 100 insert distance)