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Program URL: https://github.com/dzerbino/velvet
Article URL: http://genome.cshlp.org/content/19/6/1117.long

ABSTRACT

Widespread adoption of massively parallel deoxyribonucleic
acid (DNA) sequencing instruments has prompted the recent
development of de novo short read assembly algorithms. A
common shortcoming of the available tools is their inability
to efficiently assemble vast amounts of data generated from
large-scale sequencing projects, such as the sequencing of
individual human genomes to catalog natural genetic
variation. To address this limitation, we developed ABySS
(Assembly By Short Sequences), a parallelized sequence
assembler. As a demonstration of the capability of our
software, we assembled 3.5 billion paired-end reads from the
genome of an African male publicly released by Illumina,
Inc. Approximately 2.76 million contigs ≥100 base pairs (bp)
in length were created with an N50 size of 1499 bp,
representing 68% of the reference human genome. Analysis of
these contigs identified polymorphic and novel sequences not
present in the human reference assembly, which were
validated by alignment to alternate human assemblies and to
other primate genomes.

NOTES

ABySS allows for the computatin of the assembly in a
parallel environment, which can be an advantage over Velvet
when working with large genomes. An ABySS assembly can be
obtained with only one command that requires the k-mer
length (k), the input sequence file(s), and the name of the
output file. For paired-end reads, the minimum number of
pairs required to join two contigs (n) also needs to be
specified.

#############
# Run ABySS #
#############

$ abyss-pe k=31 n=10 in='long_1.fastq long_2.fastq' name=replica01_k31_n10

This command will output four files: *-contigs.fa (contains
contigs), *-bubbles.fa (variant sequences equal lengths),
*-indel.fa (variant sequences with different lengths),
*-contigs.dot (indicates which contigs overlap and by how
much).

################
# Output stats #
################

ABySS will not automatically output a file with assembly
statistics like Velvet's Log file. A stats file can be
generated with abyss-fac command.

$ abyss-fac replica01_k31_n10-contigs.fa > replica01_k31_n10-stats.txt

abyss-fac computes these statistics for the contigs larger
than 100 nucleotides. We achieved a similar situation with
Velvet with the option "-min_contig_lgth 100".