ABySS - assemble short reads into contigs To run ABySS: * Single-end assembly Assemble short reads in a file named reads.fa into contigs in a file named contigs.fa with the following command: ABYSS -k25 reads.fa -o contigs.fa where -k is an appropriate k-mer length. The only method to find the optimal value of k is to run multiple trials and inspect the results. The following shell snippet will assemble for every value of k from 20 to 40. for k in {20..40}; do ABYSS -k$k reads.fa -o contigs-k$k.fa done The maximum value for k is 64. This limit may be changed at compile time using the --enable-maxk option of configure. It may be decreased to 32 to decrease memory usage, which is particularly useful for large parallel jobs, or increased to 96. * Paired-end assembly To assemble paired short reads in two files named reads1.fa and reads2.fa into contigs in a file named ecoli-contigs.fa, run the command: abyss-pe k=25 n=10 in='reads1.fa reads2.fa' name=ecoli where k is the k-mer length as before. n is the minimum number of pairs needed to consider joining two contigs. The optimal value for n must be found by trial. in specifies the input files to read, which may be in FASTA, FASTQ, qseq, export, SAM or BAM format and compressed with gz, bz2 or xz and may be tarred. The assembled contigs will be stored in ${name}-contigs.fa. The suffix of the read identifier for a pair of reads must be one of '1' and '2', or 'A' and 'B', or 'F' and 'R', or 'F3' and 'R3', or 'forward' and 'reverse'. The reads may be interleaved in the same file or found in different files. If the mates are in different files, it's highly recommended to place each pair of files adjacent on the command line and to use an even number of threads. Even if you are running on a single-processor machine, using two threads will help performance. Do not group together all the files containing the forwards reads followed by all the files containing the reverse reads. Reads without mates should be placed in a file specified by the `se' (single-end) parameter. Reads without mates in the paired-end files will slow down the paired-end assembler considerably during the ParseAligns stage. abyss-pe is a driver script implemented as a Makefile and runs a single-end assembly, as described above, and the following commands, which must be found in your PATH: ABYSS - the single-end assembler AdjList - finds overlaps of length k-1 between contigs PopBubbles - collapses variation KAligner - aligns reads to contigs ParseAligns - finds pairs of reads in alignments DistanceEst - estimates distances between contigs Overlap - find overlaps between blunt contigs SimpleGraph - finds paths between pairs of contigs MergePaths - merges consistent paths Consensus - for a colour-space assembly, convert the colour-space contigs to nucleotide contigs * Paired-end assembly of multiple fragment libraries The distribution of fragment sizes of each library is calculated empirically by aligning paired reads to the contigs produced by the single-end assembler, and the distribution is stored in a file with the extension .hist, such as ecoli-4.hist. The N50 of the single-end assembly must be well over the fragment-size to obtain an accurate empirical distribution. Here's an example scenario of assembling a data set with two different fragment libraries and single-end reads: Library lib1 has reads in two files, lib1_1.fa and lib1_2.fa. Library lib2 has reads in two files, lib2_1.fa and lib2_2.fa. Single-end reads are stored in two files se1.fa and se2.fa. The command line to assemble this example data set is... abyss-pe -j j=2 k=25 n=10 name=ecoli lib='lib1 lib2' \ lib1='lib1_1.fa lib1_2.fa' lib2='lib2_1.fa lib2_2.fa' \ se='se1.fa se2.fa' The paired-end assembly of lib1 and lib2 may be run in parallel by specifying the -j option of make to abyss-pe, which is implemented as a Makefile script. One instance of KAligner is run per library, and the parameter j=2 specifies that each instance of KAligner should use two threads. The empirical distribution of fragment sizes will be stored in two files named lib1-3.hist and lib2-3.hist. These files may be plotted to check that the empirical distribution agrees with the expected distribution. The assembled contigs will be stored in ${name}-contigs.fa. * Parallel assembly The `np' option of abyss-pe specifies the number of processes to use for the ABYSS-P parallel MPI job. Without any MPI configuration, this will allow you to make use of multiple cores on a single machine. To use multiple machines for assembly, you must create a hostfile for mpirun, which is describe in the mpirun man page. The paired-end assembly runs on a single machine. For very large jobs, a good portion of the paired-end assembly (KAligner, ParseAligns, DistanceEst) may be run in parallel separate processes, but this process is not automated by the driver script abyss-pe. Open MPI integrates well with SGE (Sun Grid Engine). For example, to submit an array of jobs to assemble every odd value of k between 51 and 63 using 64 processes for each job: qsub -pe openmpi 64 -t 51-63:2 -N testing abyss-pe in=reads.fa n=10 For more information on using SGE and qsub, please refer to the qsub manual page. Open MPI must have been compiled with support for SGE using the ./configure --with-sge option. * See also Try `ABYSS --help' for more information on command line options, or see the manual page in the files `ABYSS.1' and `abyss-pe.1'. Please refer to the mpirun manual page for information on configuring parallel jobs. Written by Jared Simpson and Shaun Jackman. Subscribe to the users' mailing list at http://groups.google.com/group/abyss-users Contact the users' mailing list at or the authors directly at .