It allows to generate multiple assemblies (with different parameters and different tools) from one command It is based on VGP-pipeline (bionano scaffolding was not included) and Rapid curation but with multiple additions for QC and evaluation
If you wish to run it using conda via snakemake, then you will need:
- conda
- mamba
- snakemake
- FCS database and FCS_GX singularity container # optional
- FCS_adapter singularity container # optional
- Kraken databases # optional
- RapidCuration singularity containers # this dependency will be excluded soon
| Datatypes | read QC | read filtration | contamination check | ec | contig | purge_dups | hic qc | hic scaffolding | curation | gap_closing | qc |
|---|---|---|---|---|---|---|---|---|---|---|---|
| hifi + hic | v | v | v | v | v | v | v | v | v | v | |
| hifi + hic (no phasing) | v | v | v | v | v | v | v | v | v | v | |
| hifi + nanopore + hic | v | v | v | v | v | v | v | v | v | v | |
| hifi | v | v | v | v | v | v | NA | NA | v | ||
| clr | v | v | v | NA | NA | ||||||
| nanopore | v | v | v | NA | NA | ||||||
| illumina | v | v | v | NA | NA | ||||||
| nanopore + illumina | v | v | v | NA | NA | ||||||
| nanopore + illumina + hic | v | v | v | ||||||||
| clr + illumina | v | v | v | NA | NA | ||||||
| clr + illumina + hic | v | v | v | ||||||||
| assembly | NA | NA | v | NA | NA | NA | NA | NA | NA | v | v |
| assembly + hic | |||||||||||
| assembly + nanopore + hic | NA | ||||||||||
| assembly + hifi + hic | NA | v | v |
| Assembler | Datatypes | Status |
|---|---|---|
| hifiasm | hifi + hic | v |
| hifiasm | hifi | v |
| hifiasm | hifi + nanopore + hic | v |
| hifiasm | hifi + nanopore | v |
| hicanu | nanopore | |
| flye2 | nanopore | |
| IPA | nanopore | |
| SmartDenovo | nanopore | |
| MaSurCa | nanopore + Illumina |
I. Clone this repository
git clone https://github.com/mahajrod/AssemblyBrute
II. Place you fastqs in corresponding folders in the input directory:
AssemblyBrute/
input/
hic/
fastq/
hifi/
fastq/
nanopore/
fastq/
illumina/
fastq/
III. Modify config files. I recommend to copy default.yaml and do all modifications in this copy.
config/
default.yaml <----- modify this file, add paths to databases, set tax_id, ploidy, etc
core.yaml <----- modify this file only if you know what you are doing. In most case you don't need it
Some of the options (all nonested options from default.yaml) could also be set via command line. See examples before
IV. Run pipeline directly or via wrapper script (Not written yet). See examples below
snakemake --cores 60 --configfile config/default.yaml --printshellcmds --latency-wait 30 --config mode="assembly" "assembly_mode"="hic_scaffolding" "parameter_set"="normal" "busco_lineage_list"='["vertebrata_odb10","actinopterygii_odb10"]' "data_types"="hifi,hic" "tax_id"=206126 "use_existing_envs"=False --latency-wait 30 --use-conda --rerun-incomplete --res fcs=1 fcs_adaptor=1 mem=800000 kmer_counter=1 telosif=1
snakemake --cores 70 --configfile config/default.yaml --printshellcmds --latency-wait 60 --config mode="purge_dups" "parameter_set"="big" "data_types"="hifi,hic "use_existing_envs"=False "skip_busco"=True --use-conda --rerun-incomplete --res fcs=1 fcs_adaptor=1 mem=800000 kmer_counter=1 telosif=1
snakemake --cores 140 --configfile config/test1.yaml --printshellcmds --latency-wait 60 --config mode="assembly" assembly_mode="curation" "parameter_set"="micro" "data_types"="hifi,hic" "tax_id"=4932 "use_existing_envs"=False "skip_busco"=True "final_kmer_datatype"="hifi" "busco_lineage_list"='["saccharomycetes_odb10"]' "skip_gcp"=True --use-conda --rerun-incomplete --res fcs=1 fcs_adaptor=1 mem=800000 kmer_counter=1 telosif=1
snakemake --cores 60 --configfile config/default.yaml --printshellcmds --latency-wait 60 --config mode="qc" "parameter_set"="large" "data_types"="illumina" "tax_id"=30532 "use_existing_envs"=False "skip_busco"=True "skip_kraken"=True "skip_gcp"=True "final_kmer_datatype"="illumina" --use-conda --rerun-incomplete --res hifiasm=1 fcs=1 fcs_adaptor=1 mem=800000 kmer_counter=1
#shark
git pull; snakemake --cores 80 --configfile config/somniosus.yaml --printshellcmds --latency-wait 60 --config mode="assembly" assembly_mode="contig" "parameter_set"="giant" "data_types"="hifi,hic" "tax_id"=191813 "use_existing_envs"=False "skip_busco"=True "final_kmer_datatype"="hifi" "busco_lineage_list"='["vertebrata_odb10"]' "skip_gcp"=True --use-conda --rerun-incomplete --res fcs=1 fcs_adaptor=1 mem=800000 kmer_counter=1 telosif=1
snakemake --profile /projects/mjolnir1/people/xsg178/analysis/yggdrasil/assembly/somniosus_microcephalus_male/profile/slurm/ --configfile config/somniosus_male.yaml --printshellcmds --latency-wait 60 --config mode="assembly" assembly_mode="purge_dups" "parameter_set"="large" "data_types"="hifi,hic" "use_existing_envs"=False "skip_gcp"=True tax_id=191813 "skip_busco"=True "busco_lineage_list"='["vertebrata_odb10"]' "skip_kraken"=True --use-conda --rerun-incomplete --cluster-cancel scancel --res fcs=1 fcs_adaptor=1 telosif=1 -R get_purge_dups_read_stat
cd /maps/projects/codon_0000/people/svc-rapunzl-smrtanl/yggdrasil/assembly/fish/spinachia_spinachia_2_finalization
git pull; snakemake --cores 35 --configfile config/finalization.yaml --printshellcmds --latency-wait 60 --config mode="finalization" finalization_mode="curation" "parameter_set"="small" "data_types"="hifi,hic" "use_existing_envs"=False "skip_fcs"=True "skip_fcs_adaptor"=True "skip_read_qc"=True "skip_filter_reads"=True tax_id=206126 "busco_lineage_list"='["vertebrata_odb10", "actinopterygii_odb10"]' "skip_busco"=False "skip_higlass"=False --use-conda --rerun-incomplete --res hifiasm=1 fcs=1 fcs_adaptor=1 telosif=1 mem=700000
git pull; snakemake --cores 35 --configfile config/data/syngnathus_typhle.yaml --printshellcmds --latency-wait 60 --config mode="assembly" assembly_mode="curation" "parameter_set"="small" "data_types"="hifi,hic" "use_existing_envs"=False "skip_fcs"=False "skip_fcs_adaptor"=False tax_id=161592 "busco_lineage_list"='["vertebrata_odb10"]' "skip_busco"=False "skip_higlass"=True --use-conda --rerun-incomplete --res fcs=1 fcs_adaptor=1 telosif=1 mem=700000
sled_dog git pull; snakemake --profile /projects/mjolnir1/people/xsg178/analysis/yggdrasil/assembly/lycaon_pictus/profile/slurm --configfile config/sled_dog_mjolnir.yaml --printshellcmds --latency-wait 60 --config mode="assembly" assembly_mode="curation" "parameter_set"="big" "data_types"="hifi,hic" "use_existing_envs"=False tax_id=9615 "busco_lineage_list"='["carnivora_odb10"]' skip_busco=False skip_higlass=True --cluster-cancel scancel --use-conda --rerun-incomplete --res fcs=1 fcs_adaptor=1 telosif=1
git pull; snakemake --cores 100 --configfile config/data/PolTyp1.yaml --printshellcmds --latency-wait 60 --config mode="assembly" "assembly_mode"="curation" finalization_mode="curation_only" skip_higlass=True --use-conda --rerun-incomplete --res fcs=1 fcs_adaptor=1 telosif=1 mem=700000
#Stage by stage (recommended)
#qc and filtering
#contig assembly
#purge dups
#purge_dups with calcuts thresholds adjusted, skip if the thresholds correspond to plots
# hic scaffolding
# curation
# finalization