Implement FRC Curves

We will implement the FRC curves into Metacompass, according to the document attached.

The features we are interested in are:

• LOW_COV_PE – areas of low read coverage.
• HIGH_COV_PE – areas of high read coverage.
• LOW_NORM_COV_PE – areas of low paired-read coverage (coverage for correctly aligned paired reads).
• HIGH_NORM_COV_PE – areas of high paired-read coverage (coverage for correctly aligned paired reads).
• COMPR_PE – areas of low compression/expansion statistics.
• STRETCH_PE – areas of high compression/expansion statistics.
• HIGH_SINGLE_PE – areas of high number of reads with unmapped pair.
• HIGH_SPAN_PE – areas of high number of reads with pair mapped in a different contig/scaffold.
• HIGH_OUTIE_PE – areas of high number of mis-oriented or too distant paired reads.

Document_S1__1_.pdf

There is an output directory, /fs/cbcb-scratch/jhauzel/metacompass/final_tests/metacompass_out_sha, that should contain all of the information necessary to generate the curves.

Inputs:

• /fs/cbcb-lab/mpop/Fraunhofer_metagenomics/Shakya_sample/SRR606249_1.fastq
• /fs/cbcb-lab/mpop/Fraunhofer_metagenomics/Shakya_sample/SRR606249_2.fastq

Outputs:

• Ref-guided assembly:
  • Input Reads (currently just 1 set of paired-end reads): /fs/cbcb-scratch/jhauzel/metacompass/final_tests/metacompass_out_sha/reference_culling/align_reads/GCF_002368015.1/reads_mapped.*.fq
  • References: /fs/cbcb-scratch/jhauzel/metacompass/final_tests/metacompass_out_sha/reference_culling/collect_refs/ncbi_dataset/data
  • Contigs per reference (currently just 1 reference): /fs/cbcb-scratch/jhauzel/metacompass/final_tests/metacompass_out_sha/reference_assembly/pilon
• Denovo-guided assembly:
  • Input Reads: /fs/cbcb-scratch/jhauzel/metacompass/final_tests/metacompass_out_sha/reference_culling/align_reads/GCF_002368015.1/reads_unmapped.*.fq
  • Contigs: /fs/cbcb-scratch/jhauzel/metacompass/final_tests/metacompass_out_sha/denovo_assembly/megahit/final.contigs.fa