|
mwga-utils
|
public |
Collection of utilities for processing Multispecies Whole Genome Alignments
|
2024-12-12 |
|
renano
|
public |
RENANO is a FASTQ lossless reference-based compression algorithm especially designed for nanopore sequencing FASTQ files.
|
2024-12-12 |
|
ucsc-nettobed
|
public |
Convert target coverage of net to a bed file.
|
2024-12-12 |
|
skc
|
public |
Shared k-mer content between two genomes
|
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 |
|
psmc
|
public |
This software package infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model
|
2024-12-12 |
|
faqcs
|
public |
Quality Control of Next Generation Sequencing Data.
|
2024-12-12 |
|
samhaplotag
|
public |
Processes haplotag barcodes in SAM format.
|
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 |
|
pbsim2
|
public |
PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores
|
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 |
|
r-acidgenerics
|
public |
S4 generic functions for Acid Genomics packages.
|
2024-12-12 |
|
uvaia
|
public |
Reference-based alignment and sequence database search
|
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 |
|
r-tftargets
|
public |
Human transcription factor target genes.
|
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 |
|
ont_vbz_hdf_plugin
|
public |
VBZ compression plugin for nanopore signal data
|
2024-12-12 |
|
chromsize
|
public |
just get your chrom sizes
|
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 |
|
physlr
|
public |
Physlr; Next-generation Physical Maps
|
2024-12-12 |
|
mawk
|
public |
mawk is an interpreter for the AWK Programming Language.
|
2024-12-12 |
|
quickmerge
|
public |
Quickmerge uses a simple concept to improve contiguity of genome assemblies based on long molecule sequences.
|
2024-12-12 |
|
viennarna
|
public |
ViennaRNA package -- RNA secondary structure prediction and comparison
|
2024-12-12 |
|
emerald
|
public |
Unlocking the suboptimal pairwise alignment space for protein sequences
|
2024-12-12 |
|
pgrc
|
public |
A tool for compressing the DNA stream of FASTQ datasets.
|
2024-12-12 |
|
r-vision
|
public |
A high-throughput and unbiased module for interpreting scRNA-seq data.
|
2024-12-12 |
|
edena
|
public |
No Summary
|
2024-12-12 |
|
stark
|
public |
A tool for bluntifying a bidirected de bruijn graph by removing overlaps.
|
2024-12-12 |
|
fastutils
|
public |
A light toolkit for parsing, manipulating and analysis of FASTA and FASTQ files
|
2024-12-12 |
|
floria
|
public |
Floria is method for recovering strain-level haplotypes and clusters of reads from metagenomic short or long read sequencing data by haplotype phasing.
|
2024-12-12 |
|
fastme
|
public |
a comprehensive, accurate and fast distance-based phylogeny inference program.
|
2024-12-12 |
|
alder
|
public |
The ALDER software computes the weighted linkage disequilibrium (LD) statistic for making inference about population admixture
|
2024-12-12 |
|
pblat
|
public |
blat with multi-threads support
|
2024-12-12 |
