M.tuberculosis-variant-calling-and-gene-prediction/.gitignore at main · saleha-zip/M.tuberculosis-variant-calling-and-gene-prediction · GitHub

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# Raw sequencing reads (too large, download from SRA: ERR181435)
*.fastq
*.fastq.gz
reads_1.fastq
reads_2.fastq
ERR181435.fastq

# Reference genome and BWA index files (download from NCBI: GCF_000195955.2)
*.fna
*.fna.amb
*.fna.ann
*.fna.bwt
*.fna.pac
*.fna.sa
*.fna.fai
*.fai

# Alignment files (regenerate with: bwa mem + samtools)
*.sam
*.bam
*.bam.bai
dedup.bam

# Raw protein FASTAs (download from NCBI datasets)
mtb.faa
mbovis.faa
msmeg.faa

# GFF annotation (download from NCBI: GCF_000195955.2)
genomic.gff

# Large REvolutionH-tl intermediate outputs
tl_project.alignment_all_vs_all/

# Zone identifier files (Windows artifact)
*:Zone.Identifier

# Misc
fixed.vcf
annotated.vcf