| Package Name | Access | Summary | Updated |
|---|---|---|---|
| ucsc-twobitdup | public | check to see if a twobit file has any identical sequences in it | 2025-06-27 |
| ucsc-xmltosql | public | Convert XML dump into a fairly normalized relational database. | 2025-06-27 |
| ucsc-twobitmask | public | Apply masking to a .2bit file, creating a new .2bit file. | 2025-06-27 |
| ucsc-wigcorrelate | public | Produce a table that correlates all pairs of wigs. | 2025-06-27 |
| ucsc-validatemanifest | public | Validates the ENCODE3 manifest.txt file. | 2025-06-27 |
| ucsc-toupper | public | Convert lower case to upper case in file. Leave other chars alone. | 2025-06-27 |
| ucsc-validatefiles | public | Validates the format of different genomic files. | 2025-06-27 |
| ucsc-trfbig | public | Mask tandem repeats on a big sequence file. | 2025-06-27 |
| ucsc-transmappsltogenepred | public | Convert PSL alignments of mRNAs to gene annotations. | 2025-06-27 |
| ucsc-wordline | public | Chop up words by white space and output them with one. | 2025-06-27 |
| fgap | public | FGAP: an automated gap closing tool | 2025-06-27 |
| fastq-and-furious | public | Fast handling of FASTQ files | 2025-06-27 |
| ucsc-psltobigpsl | public | Converts psl to bigPsl input (bed format with extra fields). | 2025-06-27 |
| ucsc-fetchchromsizes | public | Used to fetch chrom.sizes information from UCSC for the given <db>. | 2025-06-27 |
| ucsc-tolower | public | Convert upper case to lower case in file. Leave other chars alone. | 2025-06-27 |
| last | public | LAST finds & aligns related regions of sequences. | 2025-06-27 |
| blastbesties | public | Rapid discovery of reciprocal best blast pairs from BLAST output files. | 2025-06-27 |
| masurca | public | MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software. | 2025-06-26 |
| ucsc-bigwigaverageoverbed | public | Compute average score of big wig over each bed, which may have introns. | 2025-06-26 |
| ucsc-bedsort | public | Sort a .bed file by chrom,chromStart. | 2025-06-26 |
| ucsc-xmlcat | public | Concatenate xml files together, stuffing all records inside a single outer tag. | 2025-06-26 |
| ucsc-bigbedsummary | public | Extract summary information from a bigBed file. | 2025-06-26 |
| ucsc-bigbedinfo | public | Show information about a bigBed file. | 2025-06-26 |
| ucsc-bedclip | public | Remove lines from bed file that refer to off-chromosome locations. | 2025-06-26 |
| fasta_ushuffle | public | a wrapper for uShuffle | 2025-06-26 |
