TULIP - The Uncorrected Long read Integration Pipeline
TULIP currently consists of two Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as...ons are likely to follow. Tulipseed takes as input alignments files of long reads to s...2239 days ago
2231 days ago
SOAP2 : Short Oligonucleotide Analysis Package 2
SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It...st and accurate alignment for huge amounts of short reads generated by Illumina/Solexa...uire only 2 minutes aligning one million single-end reads onto...2231 days ago
minialign: fast and accurate alignment tool for PacBio and Nanopore long reads
Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.2230 days ago
pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Com...2230 days ago
GenomeMapper: Simultaneous alignment of short reads against multiple genomes
GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes s...2229 days ago
WhatsHap: fast and accurate read-based phasing
WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype as...ut works also well with short reads. Features Very accur...g) Works well with Illumina, PacBio, Oxford Nanopore and other types of reads It phases SNVs, indels and...2226 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the o...op, M., Koren, S., Bickhart, D., & Chin, C. S. (2017). Scaffolding of long read assem...2208 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
git clone https://github.com/lh3/minimap2 cd minimap2 && m..../minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam # PacBio genomic reads ./minimap2 -ax map-ont ref....# Oxford Nanopore genomic reads ./minimap2 -ax sr ref.fa re...ads.fa > overlaps.paf # PacBio read overl...2203 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once d...Browse has no back-end server code, just tools for formatting data files to be read direc...2194 days ago