Use when converting Illumina BCL (Binary Base Call) files to FASTQ format using BCL Convert, the successor to bcl2fastq. Supports all modern Illumina platforms including NovaSeq X, NovaSeq X Plus, Nov
Use with AI
Install the MCP server or CLI to instantly fetch BCL Convert documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/bcl-convert
docker pull biocontainers/bcl-convert:4.4.6Chopper — fast Rust-based quality, length, and GC content filtering and trimming tool for long-read sequencing data (Oxford Nanopore, PacBio) in FASTQ format. Successor to NanoFilt with multithreaded
1 shared topic • 1 shared operation
fastools — A Python-based toolkit by Jeroen F.J. Laros for the manipulation and characterization of FASTA and FASTQ files. Use when performing sequence conversions, filtering by length, generating seq
1 shared topic • 1 shared operation
fastp — ultra-fast all-in-one FASTQ preprocessor for quality control, adapter trimming, quality filtering, per-read trimming, polyG/polyX removal, UMI processing, base correction, deduplication, and c
1 shared topic • 1 shared operation
pigz (Parallel Implementation of GZip) — multi-threaded drop-in replacement for gzip that compresses and decompresses files using multiple CPU cores. Supports gzip, zlib, and single-entry zip formats.
1 shared topic • 1 shared operation
PRINSEQ++ — high-performance C++ tool for quality control and preprocessing of FASTQ sequencing reads. Filters and trims reads by quality score, length, GC content, sequence complexity (DUST/entropy),
1 shared topic • 1 shared operation