Scripts for Vahine metagenomics and metatranscriptomics:

• generate_ACT_comparison_crunch.sh: given two genome in fasta format, generate the ACT comparison file.

• reorder_gbk_according_to_fna.py: given a ordered fna file (usually generated by Mauve), order the genbank file based on the contig order in the fna file, which can be loaded into Mauve to do genome alignment.

• download_extract_virus_fna.sh: automaticlly pull all virus genomes from NCBI, then extract the fna files.

• extract_pe_fastq_by_contigs.py: given a SAM file, a subset of reference contigs in fasta format, fwd and rev fastq reads, extract the read pairs aligned to the subset contigs.

• slice_bam_by_contigs.sh: given a BAM file and a subset of reference contigs in fasta format, slice bam to keep records aligned to the reference contigs.

• calc_cov.sh: given a subset of reference contigs in fasta format, the forward and reverse reads in fastq format, calculate the read coverage for each contig.

• calc_cov_in_bam_depth.py: script to calculate coverage of each contig in a samtools depth file. It was embedded into calc_cov.sh, but can also be used standalone.