sag_mg_recruit

chop_reads.py: chop reads into smaller reads. Use for 454 or sanger read library to approximate read size distribution of illumina library.

• Development of script can be seen in the notebook metagenome_adjustment.ipynb

rcov2.py: calculate SAG coverage using bwa, samtools and bedtools

workup_functions.py: functions used to work up the results of rcov2.py

mp_recruit.py: script to join metagenomic reads and compare them to all SAGs within designated directory using bbmap (we will not be using this in the full pipeline)

sample.py: script to randomly sample a subset of reads from a metagenome

fasta_to_fastq.py: script to create a fastq file from a .fasta and .qual file from 454 sequencing

• uses biopython, which is not available for python 3.5