rkajitani / checkmeta

CheckMeta is a method to check comprehensiveness of whole meta-genome shotgun data.

CheckMeta

CheckMeta is a method to evaluate comprehensiveness of whole meta-genome shotgun data.

input files

input files are too large to push to this repository. therefore, please refer to directories on the itoh-lab server.

core kaiju

/data2/takumi/metagenome_analysis/final_results/core_kaiju/bov2_${position}_corepfam.out
/data2/takumi/metagenome_analysis/final_results/core_kaiju/bov2_${position}_corepfam_species.txt

fastq

/data1/kajitani/denovo/Bovine_GIT/data/bov2_${position}/PE/PE_R1.fastq.trimmed
/data1/kajitani/denovo/Bovine_GIT/data/bov2_${position}/PE/PE_R2.fastq.trimmed

fasta

/data2/takumi/scratch/workspace/assembly/${position}_finalseq.fa

※position: rumen -> ru, reticulum -> re, omasum -> om, abomasum -> ab, small intestine -> si, large intestine -> li,