modules/cobrameta
A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.
Description
A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.
Input
Assembly file (contigs/scaffolds) in FASTA format
*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz} TSV file with 2 columns containing 1) the contig/scaffold id and
2) the coverage depth of the sequence specified in column 1
*.{tsv,txt} File containing the query contigs that the user wants COBRA to extend. This
can be provided in one-column TXT or FASTA format. (The IDs must match the IDs
in the --fasta file exactly)
*.{txt,fasta} Sorted BAM/CRAM/SAM file resulting from mapping reads used in assembly
to the resulting assembly FASTA
*.{bam,cram,sam} Output
Gzipped FASTA file containing query contigs that are already circular
${prefix}/COBRA_category_i_self_circular.fasta.gz Gzipped FASTA file containing query contigs that were joined and extended
into a circular genome
${prefix}/COBRA_category_ii-a_extended_circular_unique.fasta.gz Gzipped FASTA file containing query contigs were joined and extended, but
not into circular sequences
${prefix}/COBRA_category_ii-b_extended_partial_unique.fasta.gz Gzipped FASTA file containing query contigs that could not be extended due
to COBRA rules
${prefix}/COBRA_category_ii-c_extended_failed.fasta.gz Gzipped FASTA file containing query contigs that do not shared the
”expected overlap length” with other contigs
${prefix}/COBRA_category_iii_orphan_end.fasta.gz Gzipped FASTA file containing all FASTA outputs combined into one file
${prefix}/COBRA_all_assemblies.fasta.gz TSV file containing information regarding COBRA’s extension results
${prefix}/COBRA_joining_summary.txt 