BinSPreader read acquisition question

[aababc1]

Thank you very much for your hard and nice work for BinSpreader.

I used BinSPreader to improve bins got using METABAT2. ( The raw metagenome paried fastq was quality-controlled. I used metaSPAdes to get scaffolds.fa and gfa file ) .

I got binning.tsv table. It seems to be that they only get header information like below example.

$head binning.tsv
NODE_1_length_606266_cov_11.265954 bin.9.fa
NODE_2_length_403483_cov_13.852217 bin.32.fa
NODE_3_length_375106_cov_96.289678 bin.17.fa
NODE_4_length_326388_cov_38.813120 bin.71.fa
NODE_5_length_325088_cov_8.357164 bin.94.fa
NODE_6_length_309800_cov_102.246470 bin.17.fa

It there any suggested way to get improved bins using BinSPreader using binining.tsv results?

Thank you very much.

[asl]

Sure. There are lots of scripts around there. E.g. https://github.com/cmks/DAS_Tool/blob/master/src/Contigs2Bin_to_Fasta.sh

[aababc1]

Thank you so much for your quick reply.
It worked perfectly well.

[ebi-jlu8]

I have a followup question. I am using binspreader to improve bins I got from metawrap. I have used the Contigs2Bin_to_Fasta.sh to extract sequences from the refined binning.tsv file. I have a number of sequences which are not in the assembly.fasta but present in the assembly_scaffolds file. Is there a way to extract the matching sequence from the assembly graph (*.gfa) instead of the fasta file?

[asl]

Sorry, what is "assembly_scaffolds" file? This is not something produced by BinSPreader.

[ebi-jlu8]

Hi Anton. It's the assembly.gfa file that was produced by metaspades. I can see the header in the gfa file, but have no idea how to extract it.

[asl]

I do not know how assembly.fa corresponds to assembly.gfa in case of metawrap as they might post-process / alter the files produced by assembler. But normally (in case of SPAdes) scaffolds are represented as paths (P records) in assembly graph. So one would need to walk the segments, get the corresponding sequences, etc. It seems that MetaWRAP discards short scaffolds, I'd suggest you to take the complete file from assembler's output.

[ebi-jlu8]

Sorry. I meant to say metaspades. We used metaspades to get the output assembly_graph_with_scaffolds.gfa, contigs.fasta and scaffolds.fasta. I originally tried to recover the refined bins from the contigs.fasta file (after bin-refinement), but was missing a lot of sequences. I am not familiar with gfa files. Should I be looking in the assembly_graph_with_scaffolds.gfa file for binned sequences or contigs.fasta or scaffolds.fasta file? Thanks for your help.

[asl]

BinSPreader manual (https://cab.spbu.ru/software/binspreader/) explicitly says to bin scaffolds.