binning_benchmarking

Binning benchmarking involves the following steps

coassembly: read correction -> assembly -> mapping -> generate_abundance_matrix -> binning -> assessment

single-sample: read correction -> single-sample_assembly -> single-sampleread_mapping -> generate_abundance_matrix -> binning -> assessment

multi-sample: read correction -> sample-wise_assembly -> pool_allsampleassembly_contigs -> mapping -> generate_abundance_matrix -> binning -> split_bins -> remove_redundantbins -> assessment

Read correction

Reads correction is done by CoCo (https://github.com/soedinglab/CoCo). The correction is efficitive if k-mer counts are computed using reads pooled from all samples.

Concatenate reads for CoCo correction

cat *_reads.fq > all_reads.fq

Compute k-mer counts using dsk tool (https://github.com/GATB/dsk)

dsk -file all_reads.fq -kmer-size 41 (output: all_reads.h5)

Correct reads using CoCo

coco correction --reads all_reads.fq --counts all_reads.h5 --outdir allreads_coco_corrected (output: all_reads.corr.reads.fq)

Split reads by sample origin

splitreadsbysample <sampleid_file> <fastq_file> <outdir> (output: <sample_id>.fastq)

Assembly

MEGAHIT must be installed (https://github.com/voutcn/megahit.git)

pooled assembly

megahit --12 *_reads.fastq -t 64 --presets meta-sensitive -o megahit_out

sample-wise assembly

megahit --12 <sample_id>_reads.fastq -t 64 --presets meta-sensitive -o <sample_id>_megahit_out

cat *_megahit_out/final.contigs.fa > allcontigs_concatenatedallsamples.fa (concatenate all sample assemblies into one master file)

Mapping

Strobealign is the fast and accurate aligner. We used to obtain the abundance matrix. (https://github.com/ksahlin/strobealign.git)

mkdir samfiles

pooled assembly

strobealign -t 64 --aemb megahit_out/final.contigs.fa --eqx --interleaved <sample_id>.fastq > samfiles/abundances_<sample_id>.tsv

strobealign -t 64 megahit_out/final.contigs.fa --eqx --interleaved <sample_id>.fastq | samtools view -h -o samfiles/<sample_id>_strobealign.sam

concatenated sample-wise assembly

strobealign -t 64 --aemb allcontigs_concatenatedallsamples.fa --eqx --interleaved ${sample_id}.fastq > samfiles/abundances_<sample_id>.tsv

strobealign -t 64 allcontigs_concatenatedallsamples.fa --eqx --interleaved ${sample_id}.fastq |samtools view -h -o samfiles/<sample_id>_strobealign.sam

If you have used other aligners (eg. bowtie2, bwa-mem), use our in-house script

samtools view samfiles/<sample_id>_strobealign.sam | aligner2counts samfiles <sample_id> --only-mapids

Generate abundance matrix

python util/get_abundance_tsv.py -i <samfiles> -l <contig_length> -m <minlength|1000>

contig_length is a tab separated .txt file that should contain contig ids and length (contig_id\tlength). This file can be generated using convertfasta_multi2single executable (see README.md in util/).

inputdir is the directory of sample-wise abundance.tsv file. abundances_<sample_id>.tsv

Sort alignment files

samtools sort samfiles/<sample_id>_strobealign.sam -o samfiles/<sample_id>_strobealign_sorted.bam

Binning

Refer to benchmarking_scripts.ipynb. Ensure the order of contigs in the abundance matrix matches the assembly FASTA file.

Split bins (multi-sample binning)

By default, most deep learning methods can split bins by sample id in multi-sample binning mode (McDevol, VAMB and GenomeFace). But tools such as COMEBin and MetaBAT2 don't have an option for it. To perform splitting, use our script in util/.

python splitfasta_bysampleids.py --input_dir <bindir> --output_dir <outputdir> --format <binformat|fasta>

This script assumes that sample id is located in-between S and C characters. For example, from a contig id S1C141_284, it will detect 1 as the sample id.

Remove redundancy (multi-sample binning)

For this benchmarking, we mapped bins to source genomes for AMBER assessment as described in README.md in util/. However, it can be performed with de-replication approach dRep (https://github.com/MrOlm/drep). We leave the choice to the user.

Assessment

CheckM2

CheckM2 is a neural network-based method that estimates bin completeness and purity. (https://github.com/chklovski/CheckM2.git)

checkm2 predict --input <binning_tool>_results -o <binning_tool>_results/checkm2_results --thread 24 -x fasta

AMBER

For the binning of contigs from gold-standard sets, we used AMBER assessment. (https://github.com/CAMI-challenge/AMBER.git)

amber.py <binning_tool>_cluster.tsv -g gsa_pooled_mapping_short.binning -o amber_results

where gsa_pooled_mapping_short.binning files for marine, strain-madness and plant-associated datasets were obtained from the CAMI2 assessment study.

CheckM

CheckM is used to validate MetaBAT2 and MetaWRAP bin_refinement results. (https://github.com/Ecogenomics/CheckM.git)

checkm lineage_wf <binning_tool>_results <binning_tool>_results/checkm_results -x fasta -t 24

Reassembly (post-binning refinement)

Extract reads for each bin

For combined read fastq and mapfiles

extractreads <fullpath/binfastafolder> <allsample_mapids> <all_reads.corr.reads.fq> -f (binformat|fasta)

For sample-wise processing

for sample in samplelist;
do
    extractreads fullpath/binfastafolder ${sample}_mapids ${sample}.fastq -f (binformat|fasta);
done

allsample_mapids is a text file containing mapped read_id and contig_id separated by tab. This file can be generated using aligner2counts executable (see README.md in util/) for each sample as <sample_id>_mapids. Concatenate these sample-wise mapids to obtain allsample_mapids. From extracreads run, you will get <bin_id>.fastq. The extracted <bin_id>.fastq file will have reads from all samples.

spades.py --12 <bin_id>.fastq --trusted-contigs <bin_id>.fasta --only-assembler --careful -o <bin_id>_assembly/ -t 12 -m 128 SPAdes must be installed.

Refer to workflow_reassemble workflow to run the entire steps in a single run.

Plotting

Refer to plots.ipynb