3. Genome assembly

Illumina only datasets

There are many many assemblers, but for (basidiomycetic) fungi I recommend ABySS:

abyss-pe np=8 k=31 B=2G name=path/to/output/prefix in='path/to/reads_1.fastq.gz path/to/reads_2.fastq.gz' &> path/to/verbose.log

NOTE: Since it is always good to test your data, it is recommended to test different kmer sizes and pick the best one. The best way to do this is by write a loop script. For example, if you would like to test 15 different kmers with steps of 10 from 20 to 160:

declare -a k_list=("20" "30" "40" "50" "60" "70" "80" "90" "100" "110" "120" "130" "140" "150" "160")

for k in "${k_list[@]}"; do
   mkdir PATH/TO/OUTPUT_DIRECTORY/k$k
   abyss-pe np=8 k=$k -C PATH/TO/OUTPUT_DIRECTORY/k$k name=Ccos_symbiont_k$k in='PATH/TO/forward_paired_trimmed.fastq.gz PATH/TO/reverse_paired_trimmed.fastq.gz' se='PATH/TO/unpaired_trimmed.fastq.gz'
done

In case you would like to try SPAdes:

spades.py --pe1-1 path/to/lib1/reads_1.fastq.gz --pe1-2 path/to/lib1/reads_2.fastq.gz --pe2-1 path/to/lib2/reads_1.fastq.gz --pe2-2 path/to/lib2/reads_2.fastq.gz -o path/to/output -t XX -m XX

Oxford Nanopore only datasets

I have tried various assemblers and so far my favourite is SMARTdenovo:

smartdenovo -p PREFIX -c 1 -e zmo -t XX -J 500 PATH/TO/TRIMMED.fastq.gz > FANCYNAME.mak
make -f FANCYNAME.mak

NOTE: SMARTdenovo -h gives:

smartdenovo -h

Unknown option: h

Usage: smartdenovo.pl [options] <reads.fa>

Options:
-p STR     output prefix [wtasm]
-e STR     engine of overlaper, compressed kmer overlapper(zmo), dot matrix overlapper(dmo), [dmo]
  -t INT     number of threads [8]
-k INT     k-mer length for overlapping [16]
          for large genome as human, please use 17
-J INT     min read length [5000]
-c INT     generate consensus, [0]

Consider if you want to change -J read length to a different size, change the kmer length, or if you want to use their newer dot matrix overlapper

Hybrid assembly

Sometimes you are lucky and have both Illumina and long reads! Let’s use MaSuRCA for this:

masurca -t XX -i PATH/TO/illumina_1.fastq.gz,PATH/TO/illumina_2.fastq.gz -r PATH/TO/ont.fastq -p PATH/TO/OUTPUT/ 2>&1 | tee log_masurca.txt