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ucsc-genepredtogtf
|
public |
Convert genePred table or file to gtf.
|
2024-12-12 |
|
ucsc-taillines
|
public |
add tail to each line of file
|
2024-12-12 |
|
ucsc-mafsplitpos
|
public |
Pick positions to split multiple alignment input files
|
2024-12-12 |
|
deeptoolsintervals
|
public |
A python module creating/accessing GTF-based interval trees with associated meta-data
|
2024-12-12 |
|
r-rrbgen
|
public |
A lightweight limited functionality R bgen read/write library
|
2024-12-12 |
|
ucsc-netchainsubset
|
public |
Create chain file with subset of chains that appear in the net
|
2024-12-12 |
|
kmergenie
|
public |
KmerGenie estimates the best k-mer length for genome de novo assembly
|
2024-12-12 |
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ucsc-bedremoveoverlap
|
public |
Remove overlapping records from a (sorted) bed file. Gets rid of
|
2024-12-12 |
|
fastahack
|
public |
No Summary
|
2024-12-12 |
|
pear
|
public |
paired-end read merger
|
2024-12-12 |
|
ucsc-pslstats
|
public |
collect statistics from a psl file.
|
2024-12-12 |
|
ucsc-netfilter
|
public |
Filter out parts of net. What passes
|
2024-12-12 |
|
tssar
|
public |
No Summary
|
2024-12-12 |
|
skesa
|
public |
Strategic Kmer Extension for Scrupulous Assemblies & Sequence Assembly Using Target Enrichment
|
2024-12-12 |
|
perl-xml-libxslt
|
public |
Interface to GNOME libxslt library
|
2024-12-12 |
|
ucsc-nettobed
|
public |
Convert target coverage of net to a bed file.
|
2024-12-12 |
|
tn93
|
public |
This is a simple program meant to compute pairwise distances between aligned nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance.
|
2024-12-12 |
|
sambamba
|
public |
Tools for working with SAM/BAM data
|
2024-12-12 |
|
migraine
|
public |
Implements coalescent algorithms for maximum likelihood analysis of population genetic data. The data currently handled are allelic counts but sequences will be handled in the forthcoming version.
|
2024-12-12 |
|
bowtie2
|
public |
A fast and sensitive gapped read aligner.
|
2024-12-12 |
|
libbambamc
|
public |
No Summary
|
2024-12-12 |
|
rnasnp
|
public |
No Summary
|
2024-12-12 |
|
novoalign
|
public |
Powerful tool designed for mapping of short reads onto a reference genome from Illumina, Ion Torrent, and 454 NGS platforms
|
2024-12-12 |
|
ucsc-nettoaxt
|
public |
Convert net (and chain) to axt.
|
2024-12-12 |
|
faqcs
|
public |
Quality Control of Next Generation Sequencing Data.
|
2024-12-12 |
|
muse
|
public |
An accurate and ultra-fast somatic point mutation calling tool for whole-genome sequencing (WGS) and whole-exome sequencing (WES) data from heterogeneous tumor samples.
|
2024-12-12 |
|
ucsc-bedclip
|
public |
Remove lines from bed file that refer to off-chromosome locations.
|
2024-12-12 |
|
ucsc-toupper
|
public |
Convert lower case to upper case in file. Leave other chars alone
|
2024-12-12 |
|
ucsc-hgloadwiggle
|
public |
Load a wiggle track definition into database
|
2024-12-12 |
|
smartdenovo
|
public |
Ultra-fast de novo assembler using long noisy reads
|
2024-12-12 |
|
ucsc-headrest
|
public |
Return all *but* the first N lines of a file.
|
2024-12-12 |
|
dnp-binstrings
|
public |
Convert fasta strings into dinucleotide binary indicator string as 00101...
|
2024-12-12 |
|
ucsc-mafranges
|
public |
Extract ranges of target (or query) coverage from maf and
|
2024-12-12 |
|
ucsc-hgloadchain
|
public |
Load a generic Chain file into database
|
2024-12-12 |
|
ucsc-pslcdnafilter
|
public |
Filter cDNA alignments in psl format. Filtering criteria are comparative, selecting near best in genome alignments for each given cDNA and non-comparative, based only on the quality of an individual alignment.
|
2024-12-12 |
|
ucsc-estorient
|
public |
Read ESTs from a database and determine orientation based on estOrientInfo table or direction in gbCdnaInfo table. Update PSLs so that the strand reflects the direction of transcription. By default, PSLs where the direction can't be determined are dropped.
|
2024-12-12 |
|
ucsc-expmatrixtobarchartbed
|
public |
Generate a barChart bed6+5 file from a matrix, meta data, and coordinates.
|
2024-12-12 |
|
fastq-join
|
public |
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.
|
2024-12-12 |
|
lighter
|
public |
Lighter is a kmer-based error correction method for whole genome sequencing data
|
2024-12-12 |
|
rapidnj
|
public |
RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining. It uses an efficient search heuristic to speed-up the core computations of the neighbour-joining method that enables RapidNJ to outperform other state-of-the-art neighbour-joining implementations.
|
2024-12-12 |
|
mawk
|
public |
mawk is an interpreter for the AWK Programming Language.
|
2024-12-12 |
|
viennarna
|
public |
ViennaRNA package -- RNA secondary structure prediction and comparison
|
2024-12-12 |
|
edena
|
public |
No Summary
|
2024-12-12 |
|
fastme
|
public |
a comprehensive, accurate and fast distance-based phylogeny inference program.
|
2024-12-12 |
|
perl-bloom-faster
|
public |
Perl extension for the c library libbloom.
|
2024-12-12 |
|
emboss
|
public |
The European Molecular Biology Open Software Suite
|
2024-12-12 |
|
dnp-fourier
|
public |
Periodogram of dinucleotide frequency pattern
|
2024-12-12 |
|
disty
|
public |
Disty McMatrixface - compute a distance matrix from a core genome alignment file.
|
2024-12-12 |
|
dextractor
|
public |
Bax File Decoder and Data Compressor
|
2024-12-11 |
|
plek
|
public |
Predictor of long non-coding RNAs and mRNAs based on k-mer scheme.
|
2024-12-11 |
