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ART

art_illumina is the default illumina read simulator in mess and can generate reads with built-in or custom error profiles.

Built-in error profile

from art_illumina help: 

GA1 - GenomeAnalyzer I (36bp,44bp), GA2 - GenomeAnalyzer II (50bp, 75bp)
HS10 - HiSeq 1000 (100bp),          HS20 - HiSeq 2000 (100bp),      HS25 - HiSeq 2500 (125bp, 150bp)
HSXn - HiSeqX PCR free (150bp),     HSXt - HiSeqX TruSeq (150bp),   MinS - MiniSeq TruSeq (50bp)
MSv1 - MiSeq v1 (250bp),            MSv3 - MiSeq v3 (250bp),        NS50 - NextSeq500 v2 (75bp)
By default, mess uses the Hiseq 2500 error model to generate paired 150 bp read lengths with a mean and standard deviation fragment length of 200 and 10 respectively.

Built-in error profile, mean read length, mean and standard deviation fragment length can be changed with --error, --mean-length, --frag-len and --frag-sd respectively.

HiSeq 2000

mess test \
    --tech illumina \
    --error HS20 \
    --mean-len 100 \
    --frag-len 200 \
    --frag-sd 10 \
    --output hs20

Miseq v3

mess test \
    --tech illumina \
    --error MSv3 \
    --mean-len 250 \
    --frag-len 500 \
    --frag-sd 10 \
    --output msv3

Custom error profiles

If you want to use updated error profiles, your best bet is to use custom profiles, which can be generated using art_illumina_profiles.

Tip

art_illumina_profiles needs alignments from reference data like Genome in a bottle (GIAB). You can find bam and bam.bai in NCBI's reference samples ftp

GIAB hiseq 300x

Download forward and reverse error profiles 

curl -O https://raw.githubusercontent.com/hzi-bifo/art_illumina_profiles/master/example_profile/RMNISTHS_30xdownsample.1.txt \
    -O https://raw.githubusercontent.com/hzi-bifo/art_illumina_profiles/master/example_profile/RMNISTHS_30xdownsample.2.txt
Run test command with custom profile (maximum read length is 148bp)

mess test \
    --tech illumina \
    --custom-err RMNISTHS_30xdownsample \
    --mean-len 148 \
    --frag-len 300 \
    --frag-sd 10 \
    --output giab_hs300x

MBARC-26

CAMISIM also provides custom pre-built error profiles like the MBARC-26 error profile, which can be used by mess.

Download forward and reverse error profiles 

curl -O https://raw.githubusercontent.com/CAMI-challenge/CAMISIM/master/tools/art_illumina-2.3.6/profiles/ART_MBARC-26_HiSeq_R1.txt \
    -O https://raw.githubusercontent.com/CAMI-challenge/CAMISIM/master/tools/art_illumina-2.3.6/profiles/ART_MBARC-26_HiSeq_R2.txt

Run test command with custom profile

mess test \
    --tech illumina \
    --custom-err ART_MBARC-26_HiSeq_R \
    --mean-len 150 \
    --frag-len 270 \
    --frag-sd 27 \
    --output mbarc26