Docs validation section#302
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Replaces the NEAT 2.1 validateFQ/validateBam scripts (Python 2, broken read-name assumption, no gzip support, BAM tool was a raw hex dump not a validator) with recommended standard tools: FastQC/fastp for FASTQ, samtools quickcheck/flagstat and Picard ValidateSamFile for BAM, and bcftools stats for VCF. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Version headers: README title/intro/ToC updated from v4.4 → v4.5 - read_len default: corrected from 101 → 151 (matches from_cli defs) - coverage type: corrected from "float or integer" → "integer only" - threads: removed duplicate row from config table - off_target_scalar: removed from template_neat_config.yml (key has never existed in options.py defs; silently ignored since at least v4.3) - Added three undocumented config keys to README table: quality_offset, overwrite_output, no_coverage_bias - Added neat bacterial-wrapper section to Utilities + ToC entry Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Validated some docs and made updates where appropriate.