BLAST options, setting and defaults
...sp;is the best choice. Another sequence alignment tool that may yield different results from BLAST, and may be useful for motif searching, is FASTA. To search nonplant datasets,...1971 days ago
ARCS: scaffolding genome drafts with linked reads
ARCS requires two input files: Draft assembly fasta file Interleaved linked reads file (Barcode sequence expected in the BX tag of the read header or in the form "@readname_barcode" ; Run Long Ranger basic on raw chromium reads to produce this interleaved file)1963 days ago
MCAT: Motif Combining and Association Tool
This is a pipeline for finding motifs in fasta files.It can be run from the command line as fo...ve_seq negative_seq positional arguments:positive_seq the fasta file for the positive sequencesnegative_seq the fasta file for the negative sequenc...1937 days ago
SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, se...1930 days ago
NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
...contig at the site of an identified misassembly and will generate a new fasta file containing both the corr...t/tutorial.html nxrepair aligned_matepairs.bam assemblyfasta.fasta error_locations.csv new...1925 days ago
jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
...nts from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. G...1743 days ago
Minipolish: A tool for Racon polishing of miniasm assemblies
...great polishing tool that can be used to clean up assembly errors. It's also very fast and well suited for long-read data. However, it operates on FASTA files, not the GFA graph...1613 days ago
MGSE: Mapping-based Genome Size Estimation
MGSE can harness the power of files generated in genome sequencing projects to predict the genome size. Required are the FASTA file containing a high continuity assembly and a BAM fi...1568 days ago
Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
...ity SNPs. https://arxiv.org/abs/1809.06700 https://github.com/redayounsi/2KP2P /2kp2omp/bin/main_2kp2_K63_C2 -i fastq_files.txt -o fungus_bub.fasta -r stat_fungus.txt -c cov_fun...1557 days ago
Glia: a Graph/Smith-Waterman (partial order) aligner/realigner
...a VCF, both consuming and producing an ordered stream of BAM alignments. More at https://github.com/ekg/glia glia -f ~/human_g1k_v37.fasta -t 20:62900077-62902077 -v va...1557 days ago