ABYSS

Current version installed on Fourierseq: 1.2.7 by SPHS 6/1/11

Try "man abyss-pe" or "man ABYSS"

Basics of running (straight from the README):

• 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.