Setup: Running

Running fc_run.py

After installation, it is easy to start the assembly process like this,

    fc_run.py fc_run.cfg

Here is an example of fc_run.cfg for a small E. coli assembly:

    [General]
    # list of files of the initial subread fasta files
    input_fofn = input.fofn

    input_type = raw
    #input_type = preads

    # The length cutoff used for seed reads used for initial mapping
    length_cutoff = 12000

    # The length cutoff used for seed reads usef for pre-assembly
    length_cutoff_pr = 12000

    # Cluster queue setting
    sge_option_da = -pe smp 8 -q jobqueue
    sge_option_la = -pe smp 2 -q jobqueue
    sge_option_pda = -pe smp 8 -q jobqueue
    sge_option_pla = -pe smp 2 -q jobqueue
    sge_option_fc = -pe smp 24 -q jobqueue
    sge_option_cns = -pe smp 8 -q jobqueue

    # concurrency settgin
    pa_concurrent_jobs = 32
    cns_concurrent_jobs = 32
    ovlp_concurrent_jobs = 32

    # overlapping options for Daligner
    pa_HPCdaligner_option =  -v -dal4 -t16 -e.70 -l1000 -s1000
    ovlp_HPCdaligner_option = -v -dal4 -t32 -h60 -e.96 -l500 -s1000

    pa_DBsplit_option = -x500 -s50
    ovlp_DBsplit_option = -x500 -s50

    # error correction consensus optione
    falcon_sense_option = --output_multi --min_idt 0.70 --min_cov 4 --local_match_count_threshold 2 --max_n_read 200 --n_core 6

    # overlap filtering options
    overlap_filtering_setting = --max_diff 100 --max_cov 100 --min_cov 20 --bestn 10

In that case input.fofn contains a list of fasta files for E.coli:

ecoli.1.subreads.fasta
ecoli.2.subreads.fasta
ecoli.3.subreads.fasta

Those files can be obtained like this:

wget https://www.dropbox.com/s/tb78i5i3nrvm6rg/m140913_050931_42139_c100713652400000001823152404301535_s1_p0.1.subreads.fasta
wget https://www.dropbox.com/s/v6wwpn40gedj470/m140913_050931_42139_c100713652400000001823152404301535_s1_p0.2.subreads.fasta
wget https://www.dropbox.com/s/j61j2cvdxn4dx4g/m140913_050931_42139_c100713652400000001823152404301535_s1_p0.3.subreads.fasta