Acquire the fermi source code from the download page and compile with (
x.yis the version number):
tar -jxf fermi-x.y.tar.bz2 (cd fermi-x.y; make)
fastq-dump --split-spot SRR065390.lite.sra
Perform assembly with:
fermi-x.y/run-fermi.pl -ct8 -e fermi-x.y/fermi SRR065390.fastq > fmdef.mak make -f fmdef.mak -j 8 > fmdef.log 2>&1
The entire procedure takes about several hours with 8 CPU cores. File
fmdef.p5.fq.gz contains the final contigs. The quality line in the FASTQ-like
format gives the per-base read depth computed from non-redundant
0. In addition to this FAQ, are there any other documentations?
1. What is fermi?
Fermi is a de novo assembler for Illumina reads from whole-genome short-gun sequencing. It also provides tools for error correction, sequence-to-read alignment and comparison between read sets. It uses the FMD-index, a novel compressed data structure, as the key data representation.
2. How is fermi different from other assemblers?
For small genomes, fermi is not much different from other assemblers in terms of performance. Nonetheless, for mammalian genomes, fermi is one of the few choices that can do the job in a relatively small memory footprint. It can assemble 35-fold human data in 90GB shared memory with an overall similar contiguity and accuracy to other mainstream assemblers.
In addition to de novo assembly, fermi ultimately aims to preserve all the information in the raw reads, in particular heterozygous events. SNP and INDEL calling can be achieved by aligning the fermi unitigs to the reference genome and has been shown to be advantageous over other approaches in some aspects (see also the preprint).
3. What is the relationship between fermi and SGA?
Fermi is substantially influenced by SGA. It follows a similar workflow, including the idea of contrasting read sets. On the other hand, the internal implementation of fermi is distinct from that of SGA. Fermi is based on a novel data structure and uses different algorithms for almost every step. As to the end results, fermi has a similar performance to SGA for features shared between them, and is arguably easier to use. In all, both fermi and SGA are viable options for de novo assembly and contrast variant calling.
4. Are there release notes?
Yes, below this FAQ.
5. How to install fermi?
You may clone the fermi github repository to get the latest source code,
or acquire the source code of stable releases from the download page. You
can compile fermi by invoking
make in the source code directory. The only
library dependency is zlib. After compilation, you may copy
run-fermi.pl to your
PATH or simply use the executables in the source code
6. How to run fermi for de novo assembly?
The fermi manpage shows an example. Briefly, if you have Illumina
short-insert paired-end reads
read2.fq.gz, you can run:
run-fermi.pl -Pe ./fermi -t12 read1.fq.gz read2.fq.gz > fmdef.mak make -f fmdef.mak -j 12
to perform assembly using 12 CPU cores. The
fmdef.p5.fq.gz gives the final
contigs using the paired-end information. If you only want to correct errors,
you may use
make -f fmdef.mak -j 12 fmdef.ec.fq.gz
7. What is contrast assembly? How can I use it?
The idea of contrast assembly was first proposed and has been implemented by Jared Simpson and Richard Durbin. It works by assembling reads containing a k-mer that is present in one set of reads but absent from another set of reads. The contigs we get this way will span variants, including mutations and breakpoints, only seen from the first set of reads. Mapping the contigs back provides the locations. This approach directly focuses on the differences between read sets and helps to reduce the complication of structural variations and the imperfect reference genome.
To perform contrast assembly given two sets of reads, we need to generate
error-corrected FMD-index for both sets, use the
contrast command to pick
reads unique to one read set, and then apply the
sub command to extract
the FMD-index of selected reads. The following shows an example:
# error correction for sample1; paired reads are interleaved in sample1.fq.gz run-fermi.pl -ct12 -p sample1 sample1.fq.gz > sample1.mak make -f sample1.mak -j 12 sample1.ec.rank # error correction for sample2 run-fermi.pl -ct12 -p sample2 sample2.fq.gz > sample2.mak make -f sample2.mak -j 12 sample2.ec.rank # identify reads unique to one sample fermi contrast -t12 sample1.ec.fmd sample1.ec.rank sample1.sub sample2.ec.fmd sample2.ec.rank sample2.sub # generate the FMD-index for reads unique to sample1; similar applied to sample2 fermi sub -t12 sample1.fmd sample1.sub > sample1.sub.fmd # assemble unique reads and perform graph simplification fermi unitig -l50 -t12 sample1.sub.fmd > sample1.sub.mag fermi clean -CA -l150 sample1.sub.mag > sample1-cleaned.sub.mag
We can align the resulting contigs
sample1-cleaned.sub.mag to the reference
genome with BWA-SW to pinpoint the mutations and break points. It is also
possible to compare one sample to multiple samples by intersecting selected
reads using the
bitand command and then performs the assembly.
A more convenient command-line interface is likely to be added in future.
Release 1.1 (2012-08-22)
This release reduces the runtime of assembly by introducing an improved version of the BCR algorithm for constructing FMD-index and by deploying heuristics in error correction. On two human data sets, fermi takes 30% less wall-clock time and produces slightly longer scaftigs, though at the cost of marginally increased assembly break points in comparison to release 1.0.
(1.1: 2012-08-22, r744)
Release 1.0 (2012-04-09)
This is the first public release of fermi, a de novo assembler and analysis tool for whole-genome shot-gun sequencing. Source code can be acquired from the download page. Please read the manpage and the FAQ for detailed usage.
(1.0: 2012-04-09, r700)