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ucsc-pslmap
|
public |
map PSLs alignments to new targets using alignments of
|
2024-08-27 |
|
ucsc-sqltoxml
|
public |
dump out all or part of a relational database to XML, guided
|
2024-08-27 |
|
ucsc-subcolumn
|
public |
Substitute one column in a tab-separated file.
|
2024-08-27 |
|
ucsc-hgloadmaf
|
public |
Load a maf file index into the database
|
2024-08-27 |
|
ucsc-chromgraphfrombin
|
public |
Convert chromGraph binary to ascii format.
|
2024-08-27 |
|
ucsc-genepredtobed
|
public |
Convert from genePred to bed format. Does not yet handle genePredExt
|
2024-08-27 |
|
ucsc-ixixx
|
public |
Create indices for simple line-oriented file of format
|
2024-08-27 |
|
ucsc-bedclip
|
public |
Remove lines from bed file that refer to off-chromosome locations.
|
2024-08-27 |
|
ucsc-ldhggene
|
public |
load database with gene predictions from a gff file.
|
2024-08-27 |
|
ucsc-mafspecieslist
|
public |
Scan maf and output all species used in it.
|
2024-08-27 |
|
ucsc-mafcoverage
|
public |
Analyse coverage by maf files - chromosome by
|
2024-08-27 |
|
ucsc-parasol
|
public |
Parasol is the name given to the overall system for managing jobs on a computer cluster and to this specific command. This command is intended primarily for system administrators. The 'para' command is the primary command for users.
|
2024-08-27 |
|
ucsc-mrnatogene
|
public |
convert PSL alignments of mRNAs to gene annotations
|
2024-08-27 |
|
ucsc-mafgene
|
public |
output protein alignments using maf and genePred
|
2024-08-27 |
|
ucsc-netfilter
|
public |
Filter out parts of net. What passes
|
2024-08-27 |
|
ucsc-hgloadnet
|
public |
Load a generic net file into database
|
2024-08-27 |
|
ucsc-toupper
|
public |
Convert lower case to upper case in file. Leave other chars alone
|
2024-08-27 |
|
ucsc-genepredcheck
|
public |
validate genePred files or tables
|
2024-08-27 |
|
ucsc-genepredfilter
|
public |
filter a genePred file
|
2024-08-27 |
|
ucsc-beditemoverlapcount
|
public |
count number of times a base is overlapped by the
|
2024-08-27 |
|
ucsc-pslmrnacover
|
public |
Make histogram of coverage percentage of mRNA in psl.
|
2024-08-27 |
|
minimap2
|
public |
A versatile pairwise aligner for genomic and spliced nucleotide sequences.
|
2024-08-27 |
|
lambda
|
public |
Lambda is a local aligner optimized for many query sequences and searches in protein space
|
2024-08-26 |
|
perl-parallel-forkmanager
|
public |
A simple parallel processing fork manager
|
2024-08-26 |
|
adapterremoval
|
public |
The AdapterRemoval v2 tool for merging and clipping reads.
|
2024-08-25 |
|
hmmer
|
public |
Biosequence analysis using profile hidden Markov models
|
2024-08-24 |
|
gxformat2
|
public |
Galaxy Workflow Format 2 Descriptions
|
2024-08-23 |
|
bpipe
|
public |
Bpipe - a tool for running and managing bioinformatics pipelines
|
2024-08-23 |
|
art
|
public |
No Summary
|
2024-08-22 |
|
pyseer
|
public |
Sequence Element Enrichment Analysis (SEER), python implementation
|
2024-08-22 |
|
whatshap
|
public |
phase genomic variants using DNA sequencing reads (haplotype assembly)
|
2024-08-21 |
|
python-hyphy-python
|
public |
HyPhy package interface library
|
2024-08-21 |
|
cyvcf2
|
public |
A cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files
|
2024-08-21 |
|
bowtie2
|
public |
A fast and sensitive gapped read aligner.
|
2024-08-21 |
|
r-sigqc
|
public |
Provides gene signature quality control metrics in publication ready plots. Namely, enables the visualization of properties such as expression, variability, correlation, and comparison of methods of standardisation and scoring metrics.
|
2024-08-19 |
|
pipits
|
public |
PIPITS: An automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences from the Illumina sequencing platform
|
2024-08-19 |
|
htsbox
|
public |
HTSbox is a fork of early HTSlib. It is a collection of small experimental tools manipulating HTS-related files.
|
2024-08-16 |
|
pasta
|
public |
An implementation of the PASTA (Practical Alignment using Sate and TrAnsitivity) algorithm
|
2024-08-15 |
|
unicycler
|
public |
Hybrid assembly pipeline for bacterial genomes
|
2024-08-14 |
|
dsk
|
public |
DSK is a k-mer counter for reads or genomes.
|
2024-08-14 |
|
discosnp
|
public |
reference-free small variant caller for short read sequencing data
|
2024-08-14 |
|
lastz
|
public |
LASTZ is a program for aligning DNA sequences, a pairwise aligner.
|
2024-08-13 |
|
spades
|
public |
SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.
|
2024-08-13 |
|
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.
|
2024-08-12 |
|
pkiss
|
public |
RNA secondary structure prediction including K-type and kissing hairpin- pseudoknots.
|
2024-08-11 |
|
treetime
|
public |
Maximum-Likelihood dating and ancestral inference for phylogenetic trees
|
2024-08-11 |
|
pyani
|
public |
pyani provides a package and script for calculation of genome-scale average nucleotide identity.
|
2024-08-09 |
|
nanoplot
|
public |
Plotting suite for long read sequencing data and alignments
|
2024-08-09 |
|
comet-ms
|
public |
Comet is a command line tool that does MS/MS database search.
|
2024-08-09 |
|
fastme
|
public |
a comprehensive, accurate and fast distance-based phylogeny inference program.
|
2024-08-09 |
