The La Jolla Assembler (LJA) is a tool for assemblies of long and accurate reads. It reduces the error rate in these reads by three orders of magnitude (making them nearly error-free) and constructs the de Bruijn graph for large genomes and large k-mer sizes. Since the de Bruijn graph constructed for a fixed k-mer size is typically either too tangled or too fragmented, LJA uses a new concept of a multiplex de Bruijn graph with varying k-mer sizes.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive [user@cn3107 ~]$module load LJAAvailable executables:
[user@biowulf]$ ls $LJA_BIN dot_bulge_stats jumboDBG lja run_polishing run_tests sdbg_statsBasic usage:
[user@cn3107 ~]$lja -h LJA: genome assembler for PacBio HiFi reads based on de Bruijn graph. Usage: lja [options] -o <output-dir> --reads <reads_file> [--reads <reads_file2> ...] Basic options: -o <file_name> (or --output-dir <file_name>) Name of output folder. Resulting graph will be stored there. --reads <file_name> Name of file that contains reads in fasta or fastq format. This option can be used any number of times in the same command line. In this case reads from all specified files will be used as an input. -h (or --help) Print this help message. Advanced options: -t <int> (or --threads <int>) Number of threads. The default value is 16. -k <int> Value of k used for initial error correction. -K <int> Value of k used for final error correction and initialization of multiDBG. --diploid Use this option for diploid genomes. By default LJA assumes that the genome is haploid or inbred.Running tests:
[user@cn3107 ~]$ run_tests Running main() from /usr/local/apps/LJA/LJA/src/tests/googletest-master/googletest/src/gtest_main.cc [==========] Running 30 tests from 26 test suites. [----------] Global test environment set-up. [----------] 1 test from DB1 [ RUN ] DB1.Basic [ OK ] DB1.Basic (0 ms) [----------] 1 test from DB1 (0 ms total) [----------] 1 test from DBSingleEdge1 [ RUN ] DBSingleEdge1.Basic [ OK ] DBSingleEdge1.Basic (0 ms) [----------] 1 test from DBSingleEdge1 (0 ms total) [----------] 1 test from DBSingleEdge2 [ RUN ] DBSingleEdge2.Basic [ OK ] DBSingleEdge2.Basic (0 ms) [----------] 1 test from DBSingleEdge2 (0 ms total) [----------] 1 test from DBSingleEdge3 [ RUN ] DBSingleEdge3.Basic [ OK ] DBSingleEdge3.Basic (0 ms) [----------] 1 test from DBSingleEdge3 (0 ms total) [----------] 1 test from DBStVertex [ RUN ] DBStVertex.Basic [ OK ] DBStVertex.Basic (0 ms) [----------] 1 test from DBStVertex (0 ms total) [----------] 1 test from DBEvVertex [ RUN ] DBEvVertex.Basic [ OK ] DBEvVertex.Basic (0 ms) [----------] 1 test from DBEvVertex (0 ms total) [----------] 2 tests from DB1inVertex [ RUN ] DB1inVertex.Basic [ OK ] DB1inVertex.Basic (1 ms) [ RUN ] DB1inVertex.WithShortEdge [ OK ] DB1inVertex.WithShortEdge (0 ms) [----------] 2 tests from DB1inVertex (1 ms total) [----------] 2 tests from DB1outVertex [ RUN ] DB1outVertex.Basic [ OK ] DB1outVertex.Basic (0 ms) [ RUN ] DB1outVertex.WithShortEdge [ OK ] DB1outVertex.WithShortEdge (0 ms) [----------] 2 tests from DB1outVertex (0 ms total) [----------] 1 test from DBComplexVertex [ RUN ] DBComplexVertex.Basic [ OK ] DBComplexVertex.Basic (0 ms) [----------] 1 test from DBComplexVertex (0 ms total) [----------] 1 test from DBComplexVertexLoop1 [ RUN ] DBComplexVertexLoop1.Basic [ OK ] DBComplexVertexLoop1.Basic (0 ms) [----------] 1 test from DBComplexVertexLoop1 (0 ms total) [----------] 1 test from DBComplexVertexLoop2 [ RUN ] DBComplexVertexLoop2.Basic [ OK ] DBComplexVertexLoop2.Basic (0 ms) [----------] 1 test from DBComplexVertexLoop2 (0 ms total) [----------] 1 test from DBComplexVertexLoop3 [ RUN ] DBComplexVertexLoop3.Basic [ OK ] DBComplexVertexLoop3.Basic (0 ms) [----------] 1 test from DBComplexVertexLoop3 (0 ms total) [----------] 1 test from DBComplexVertexLoop4 [ RUN ] DBComplexVertexLoop4.Basic [ OK ] DBComplexVertexLoop4.Basic (0 ms) [----------] 1 test from DBComplexVertexLoop4 (0 ms total) [----------] 1 test from DBComplexVertexLoop5 [ RUN ] DBComplexVertexLoop5.Basic [ OK ] DBComplexVertexLoop5.Basic (1 ms) [----------] 1 test from DBComplexVertexLoop5 (1 ms total) [----------] 1 test from DBComplexVertexConn4 [ RUN ] DBComplexVertexConn4.Basic [ OK ] DBComplexVertexConn4.Basic (0 ms) [----------] 1 test from DBComplexVertexConn4 (0 ms total) [----------] 1 test from DBComplexVertexConn3 [ RUN ] DBComplexVertexConn3.Basic [ OK ] DBComplexVertexConn3.Basic (0 ms) [----------] 1 test from DBComplexVertexConn3 (0 ms total) [----------] 1 test from DBComplexVertexConn3_2 [ RUN ] DBComplexVertexConn3_2.Basic [ OK ] DBComplexVertexConn3_2.Basic (0 ms) [----------] 1 test from DBComplexVertexConn3_2 (0 ms total) [----------] 1 test from DBComplexVertexLoop6 [ RUN ] DBComplexVertexLoop6.Basic [ OK ] DBComplexVertexLoop6.Basic (0 ms) [----------] 1 test from DBComplexVertexLoop6 (0 ms total) [----------] 1 test from DBComplexVertexLoop7 [ RUN ] DBComplexVertexLoop7.Basic [ OK ] DBComplexVertexLoop7.Basic (0 ms) [----------] 1 test from DBComplexVertexLoop7 (0 ms total) [----------] 1 test from DBComplexVertexLoop8 [ RUN ] DBComplexVertexLoop8.Basic [ OK ] DBComplexVertexLoop8.Basic (0 ms) [----------] 1 test from DBComplexVertexLoop8 (0 ms total) [----------] 1 test from DBDoubleLoopRC [ RUN ] DBDoubleLoopRC.Basic [ OK ] DBDoubleLoopRC.Basic (1 ms) [----------] 1 test from DBDoubleLoopRC (1 ms total) [----------] 1 test from DBIsolate [ RUN ] DBIsolate.Basic [ OK ] DBIsolate.Basic (0 ms) [----------] 1 test from DBIsolate (0 ms total) [----------] 1 test from DBEmptyGraph [ RUN ] DBEmptyGraph.Basic [ OK ] DBEmptyGraph.Basic (0 ms) [----------] 1 test from DBEmptyGraph (0 ms total) [----------] 2 tests from RRPathsTest [ RUN ] RRPathsTest.Basic [ OK ] RRPathsTest.Basic (0 ms) [ RUN ] RRPathsTest.MergeIterDereference [ OK ] RRPathsTest.MergeIterDereference (0 ms) [----------] 2 tests from RRPathsTest (0 ms total) [----------] 1 test from EdgeSegment [ RUN ] EdgeSegment.Basic [ OK ] EdgeSegment.Basic (0 ms) [----------] 1 test from EdgeSegment (0 ms total) [----------] 2 tests from MDBGSeq [ RUN ] MDBGSeq.SingleSegment [ OK ] MDBGSeq.SingleSegment (0 ms) [ RUN ] MDBGSeq.SeveralSegments [ OK ] MDBGSeq.SeveralSegments (0 ms) [----------] 2 tests from MDBGSeq (0 ms total) [----------] Global test environment tear-down [==========] 30 tests from 26 test suites ran. (3 ms total) [ PASSED ] 30 tests.End the interactive session:
[user@cn3107 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$