| fastq-mcf |
Scans a sequence file for adapters, and, based on a log-scaled threshold, determines a set of clipping parameters and performs clipping. Also does skewing detection and quality filtering. |
| fastq-multx |
Demultiplexes a fastq. Capable of auto-determining barcode id's based on a master set fields. Keeps multiple reads in-sync during demultiplexing. Can verify that the reads are in-sync as well, and fail if they're not. |
| fastq-join |
Similar to audy's stitch program, but in C, more efficient and supports some automatic benchmarking and tuning. It uses the same "squared distance for anchored alignment" as other tools. |
| varcall |
Takes a pileup and calculates variants in a more easily parameterized manner than some other tools. |
| sam-stats |
Basic sam/bam stats. Like other tools, but produces what I want to look at, in a format suitable for passing to other programs. (View source) |
| fastq-stats |
Basic fastq stats. Counts duplicates. Option for per-cycle stats, or not (irrelevant for many sequencers). |