cobra

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Usage of cobra

2

Cobra is an interesting software, but I have some questions. Is the input data must be viral metagenome data? I'm not sure if cobra could works for common metagenome data...

quliping

Error about blastn

1

Hi Dr Chen： I try to run COBRA today with ```Shell source activate cobra cobra-meta -f Megahit_out/611PES1/611PES1_megahit.contigs.fa -q checkv_in/611RW.fa -o COBRA/611_RW_MV_COBRA -c coverage/611RW_coverage.txt -m mapping/611RW-MV.sam -a megahit -mink 21 -maxk...

Songq-20

Group Extended_partial

1

Dear developers. Could you clarify please. Why is the group Extended_partial based on checkV results circularized (with DTR)? Can I take these sequences as putative complete genomes?

SergeyBaikal

Docker/Singularity

1

Hi, Do you have any plan to release a Docker/Singularity version of COBRA? Thanks

rhernandvel

Interrogation regarding overlap-based assemblers

1

Thank you for the great tool! I am using MEGAHIT+VIBRANT+COBRA to get about 35 high-quality phages from each of my metagenomes after validation by CheckV. I just tested the new...

bhagavadgitadu22

fixed the bug in get_cov function that attempts to skip the header line, regardless if it's a header or not; also minor bugfixes

yayekit

will fix #43 ## background in the issue, queries are extended as follow pattern:  and the environment is: ```python query_set = frozenset(( "AcMG_5518", "AcMG_12242", "AcMG_3793", "AcMG_755", "AcMG_9925", "AcMG_9528")) contig2assembly...

Hocnonsense

I got the following error when running the COBRA pipeline. I have run cobra.py with other metagenomes which worked fine but had problems this particular sample. I checked that contig...

lingrongjin

KeyError

2

Hello, When I try to run cobra, I just get error message like this ``` (cobra) wk@t:~/res/20240905_cobra$ cobra-meta -f /home/wk/res/test/SPAdes/contigs.fasta -q /home/wk/res/20240905_cobra/metaSpades_contigs_top5.tsv -a metaspades -mink 21 -maxk 121 -m /home/wk/res/test/mapping/test_sorted.bam...

Syutenjyo